Xu, F et al. 2024. iFLAS: positive-unlabeled learning facilitates full-length transcriptome-based identification and functional exploration of alternatively spliced isoforms in maize. New Phytol. :doi: 10.1111/nph.19554.
   iFLAS: positive-unlabeled learning facilitates full-length transcriptome-based identification and functional exploration of alternatively spliced isoforms in maize.

Other examples of genes exhibiting allele-specific alternative splicing: Zm00001d007470, Zm00001d034313, Zm00001d035140, Zm00001d053864, Zm00001d053865, Zm00001d017303, Zm00001d000224, Zm00001d002836, Zm00001d017303, Zm00001d020178, Zm00001d040612, Zm00001d042394, Zm00001d021822

Advances in full-length transcriptome sequencing technology have accelerated the discovery of novel splice isoforms. However, current alternative splicing (AS) tools are mainly designed for human and animal studies. The differences in AS patterns between plants and animals pose a challenge to identification and functional exploration of novel isoforms in plants. This study developed a plant-optimized full-length transcriptome analysis toolkit called iFLAS, which uses a semi-supervised machine learning approach positive-unlabeled (PU) learning to accurately identify novel isoforms and enable investigation of AS functions from multiple perspectives, such as differential AS, poly(A) tail length, and allele-specific AS (ASAS) analysis. By applying iFLAS to three full-length transcriptome sequencing datasets, this study systematically identified and functionally characterized maize (Zea mays) AS patterns. The results showed that intron retention not only introduces premature termination codons, leading to reduced expression levels of the isoforms; but also regulates the length of the 3'UTR and poly (A) tails, affecting the functional differentiation of the isoforms. In addition, different ASAS patterns were observed in the hybrid offspring of maize inbred lines B73 and Ki11, highlighting their potential value in breeding. These results highlight the extensive utilization of iFLAS in research on plant full-length transcriptome alternative splicing.

Xu, F et al. 2024. iFLAS: positive-unlabeled learning facilitates full-length transcriptome-based identification and functional exploration of alternatively spliced isoforms in maize. New Phytol. :doi: 10.1111/nph.19554.
   iFLAS: positive-unlabeled learning facilitates full-length transcriptome-based identification and functional exploration of alternatively spliced isoforms in maize.
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Cao, SA et al. 2024. Cytoplasmic genome contributions to domestication and improvement of modern maize BMC Biology. 22:64.
   Cytoplasmic genome contributions to domestication and improvement of modern maize

The significance of cytoplasmic genomes to maize domestication and breeding is examined in this article. Cytoplasmic organelles (mitochondria, chloroplast) are important for growth and development, they are semi-autonomous (their own genome) with a constant rate of sequence changes in their genomes. All these characteristics suggest they may have an important role in domestication and improvement of maize. Cytoplasmic male sterility (CMS) of great importance in maize breeding is determined by mutations in the mitochondrial genome. The two male-fertility cytotypes (NA and NB) and the three main CMS types (CMS-C, CMS-T, and CMS-S) were examined here. Comparing the entire genome sequences of 630 related accessions of maize from North America and China, authors studied the contribution of cytoplasmic genomes in domestication and improvement of maize. According to the study’s findings, maize's cytoplasmic and nuclear genomes coevolved throughout domestication and improvement. Furthermore, the nucleotypic diversity among genes involved in photosynthesis, energy, and metabolism, have increased as a result of cytoplasmic genome evolution. The cytoplasmic variation in those genes is associated with key agronomic and reproductive traits. These new insights and considering cytoplasmic genome variation between genotypes can help in the improvement of yield stability and crop resilience of maize.

Cao, SA et al. 2024. Cytoplasmic genome contributions to domestication and improvement of modern maize BMC Biology. 22:64.
   Cytoplasmic genome contributions to domestication and improvement of modern maize
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Wenyu Li et al. 2024. ZmMAPK6, a mitogenactivated protein kinase, regulates maize kernel weight. J Exp Bot. :doi: 10.1093/jxb/erae104.
   ZmMAPK6, a mitogenactivated protein kinase, regulates maize kernel weight.

Understanding the biological processes that contribute to grain size and weight are important for ensuring global food security. The maize Mitogen-Activated Protein Kinase 6 (ZmMAPK6), an active kinase, has previously been shown to be involved with various biotic and abiotic stresses. The authors show that changes in ZmMAPK6 expression in mutants and overexpression lines respectively decrease or increase maize grain weight and size. Increases in weight (16-23% weight increase) and size in the overexpression lines are due to increased grain-filling, resulting in more starch and protein accumulation. Transcripts involved with seed growth and development were found to be downregulated in zmmpk6-cr mutants compared to wild type. Overall, ZmMAPK6 is a promising target to explore for maize yield improvement.

Wenyu Li et al. 2024. ZmMAPK6, a mitogenactivated protein kinase, regulates maize kernel weight. J Exp Bot. :doi: 10.1093/jxb/erae104.
   ZmMAPK6, a mitogenactivated protein kinase, regulates maize kernel weight.
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Zhong, T et al. 2024. The ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module provides quantitative resistance to gray leaf spot in maize Nature Genetics. :doi: 10.1038/s41588-023-01644-z.
   The ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module provides quantitative resistance to gray leaf spot in maize

Gray spot (GLS) is a major foliar disease of maize caused by the fungal pathogens Cercospora zeae-maydis and Cercospora zeina. Since its discovery in the United States in the 1920s, GLS has become a disease that severely affects maize yields. GLS resistance is a quantitative trait. Although more than 100 quantitative loci have been identified, the number of GLS resistance genes identified so far are very rare. In this study, a major quantitative resistance locus, qRgls1, was identified in segregating population derived from a cross between the highly GLS-resistant inbred line Y32 and GLS-susceptible inbred line Q11, this locus was able to significantly increase resistance to GLS in maize. The functional gene of this locus, ZmWAKL, was identified by fine-mapping and transgenic experiments validation, and the allele in Y32 was designated as resistant gene ZmWAKL Y , and the allele in Q11 was designated as susceptible gene ZmWAKL Q . Through further split luciferase complementation (SLC) and co-immunoprecipitation (Co-IP) experiments, it was found that ZmWAKL was able to occur homodimerization and binds to its co-receptor ZmWIK at plasma membrane to form the ZmWAKLY/ZmWIK immune complex. This complex further interacts with cytoplasmic receptor kinase ZmBLK1, which transmits the immune signals to NADPH oxidase ZmRBOH4 at plasma membrane. Upon challenge by the pathogen Cercospora zeina, the resistance gene ZmWAKL Y occurs homodimerization resulting in a rapid increase in its own phosphorylation activity, and together with ZmWIK, transmits immune signals to ZmBLK1 and then to ZmRBOH4, which triggers a ROS burst to incur innate immunity, resulting in maize disease resistance; while the susceptible gene ZmWAKL Q could not occurs homodimerization to increase its own phosphorylation activity, which impeded the signaling pathway, resulting in maize disease susceptibility. In conclusion, this study reveals the role of the maize ZmWAKL-ZmWIK-ZmBLK1-ZmRBOH4 receptor/signaling/executive module in enhancing resistance to GLS.

Zhong, T et al. 2024. The ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module provides quantitative resistance to gray leaf spot in maize Nature Genetics. :doi: 10.1038/s41588-023-01644-z.
   The ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module provides quantitative resistance to gray leaf spot in maize
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Zhou, Y et al. 2024. Genetic regulation of self-organizing azimuthal canopy orientations and their impacts on light interception in maize Plant Cell. :doi: 10.1093/plcell/koae007.
   Genetic regulation of self-organizing azimuthal canopy orientations and their impacts on light interception in maize

Increasing yields of commercial maize hybrids have been possible thanks to their improved tolerance to high plant densities. Under these circumstances plants can shade nearby plants reducing light penetration. Authors studied how maize plants adjust their canopy to tolerate the shading, finding some genotypes able to alter their azimuthal canopy orientation during development with their leaves growing in parallel to the leaves of adjacent plants. They performed a genome-wide association study on parallel canopy and on the fraction of intercepted photosynthetically active radiation. The parallel canopy trait is measured as the number or percentage of plants that are mutually parallel. They found candidate genes associated with shade avoidance syndrome and ligule development. Using mutagenesis, they demonstrated that liguleless genes (lg1, lg2, lg3) are also required for azimuthal canopy re-orientation and other normal light responses. Authors emphasize that it’s likely that pathways other than shade avoidance syndrome could also contribute to azimuthal canopy re-orientation. They also hypothesized that perception of blue light is key for the initiation of azimuthal canopy re-orientation, and this initiation signal is transduced via auxin signaling.

Zhou, Y et al. 2024. Genetic regulation of self-organizing azimuthal canopy orientations and their impacts on light interception in maize Plant Cell. :doi: 10.1093/plcell/koae007.
   Genetic regulation of self-organizing azimuthal canopy orientations and their impacts on light interception in maize
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Li, XL et al. 2024. Heat stress at the bicellular stage inhibits sperm cell development and transport into pollen tubes Plant Physiol. :doi: 10.1093/plphys/kiae087.
   Heat stress at the bicellular stage inhibits sperm cell development and transport into pollen tubes

In this article the authors have focused on understanding the development of pollen tube (male gametophyte) during the reproductive stages under heat stress. It was found that when moderate heat stress is applied to the for a period of 2 days during the uni- and bicellular stages of pollen development it severely accelerates or shortens the pollen development time and impairs the pollen germination capabilities. To get a deep understanding of this the authors set an experiment for pollinating the maize plants with heat stressed pollen and non-stressed pollen and then examine the rate of seed set through the entire cobs. These experiments suggested that the cobs pollinated with heat stressed pollens have 65% reduced seed formation compared to the control ones, suggesting that the heat stressed pollens fall into the category of non-fertile type. Further to gain insights at heat stress effects on pollen impairment based on stages i.e., uni- or bicellular morphological and biochemical experiments were performed, the findings suggests that heat stress at unicellular stage significantly effects pollen germination capabilities while the effect of heat stress at bicellular stage corresponds to affecting the sperm cell development and transport. How the sperm cell transportation ability is affected by heat stress to investigate this the mobility of the sperm cell inside the pollen tube was analyzed using α-tubulin-YFP marker line it was found that after 1 h of pollen germination and growth in vitro, about 80% non-stressed sperm cells were visible inside pollen tubes however the number was significantly reduced to 20% in case of heat-stressed conditions. Further it was found that heat-stress impacts expression of genes involved in transcription, DNA replication, RNA processing, and translation in sperm cells and this leads to mis-regulation of cell cycle control genes in the sperm cell.

Li, XL et al. 2024. Heat stress at the bicellular stage inhibits sperm cell development and transport into pollen tubes Plant Physiol. :doi: 10.1093/plphys/kiae087.
   Heat stress at the bicellular stage inhibits sperm cell development and transport into pollen tubes
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Kumar, R et al. 2023. Genetic architecture of source-sink-regulated senescence in maize. Plant Physiol. :doi: 10.1093/plphys/kiad460.
   Genetic architecture of source-sink-regulated senescence in maize.

Source (photosynthetic organs like leaves) and sink (storage organs like ear and stalk) interactions play a critical role in regulating the senescence in maize. The important role of this interactions is obvious as activity of source determines the amount of photosynthates available for the plant growth and storage, while sink activity relates to the crop yield. However, the genetic and molecular mechanism through which source-sink interactions regulates senescence were poorly understood. Kumar et al., (2023), used a systems genetics approach to understand the mechanism of source-sink regulated senescence (SSRS) induced by preventing the pollination of maize ear. Authors performed a comprehensive time course phenotypic and transcriptomic analysis. Authors comparative analysis showed that SSRS phenotypes starts with a feedback inhibition of photosynthesis, a surge in reactive oxygen species, and the resulting endoplasmic reticulum (ER) stress results from weakened sink demand. Authors performed a multi-environmental evaluation of a biparental population and a diversity panel and identified 12 quantitative trait loci and 24 candidate genes, respectively, underlying SSRS. By combining the natural diversity and coexpression networks analyses authors identified 7 high-confidence candidate genes involved in proteolysis, photosynthesis, stress response, and protein folding. Authors showed the role of a cathepsin B like protease 4 (ccp4) in SSRS, by analysis of natural alleles in maize and heterologous analyses in Arabidopsis (Arabidopsis thaliana). Finally, authors proposed a model for SSRS regulation, and their findings provide a deeper understanding of source-sink interactions. This study offers an opportunity to modify these interactions to alter senescence program and enhance crop productivity.

Kumar, R et al. 2023. Genetic architecture of source-sink-regulated senescence in maize. Plant Physiol. :doi: 10.1093/plphys/kiad460.
   Genetic architecture of source-sink-regulated senescence in maize.
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Liu, X-Y et al. 2024. Maize requires Embryo defective27 for embryogenesis and seedling development Plant Physiol. :doi: 10.1093/plphys/kiae010.
   Maize requires Embryo defective27 for embryogenesis and seedling development

The maize mutant embryo defective27 (emb27) was identified using the UniformMu mutagenesis population and found to encode the chloroplast-localized ribosomal protein RPS13. The kernels of the emb27 mutant make normal endosperm but have defects in embryo development, while a second weaker allele emb27-2, makes normal kernels but has albino seedlings due to chloroplast defects. The authors find that transcription level of Emb27 is correlated with normal embryogenesis with a minimum threshold of 6% of wild-type and that expression is likely modulated by genetic background. In addition, emb27 mutants have defects in plastid ribosome assembly and chloroplast protein translation. The emb27-1 allele and other plastid-translation-deficient mutants have splicing defects in plastid transcripts, further indicating defects in plastid translation. Altogether these data suggest a model where nuclear encoded Emb27 is expressed, translated, and imported into the plastid where it facilitates assembly of chloroplast ribosomes and translation of chloroplast proteins. Severe reduction in Emb27 transcript levels lead to embryo lethality through a hypothesized retrograde signal, providing insight into the role of plastid translation in regulating maize embryogenesis.

Liu, X-Y et al. 2024. Maize requires Embryo defective27 for embryogenesis and seedling development Plant Physiol. :doi: 10.1093/plphys/kiae010.
   Maize requires Embryo defective27 for embryogenesis and seedling development
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Yan, PS et al. 2023. Biofortification of iron content by regulating a NAC transcription factor in maize Science. 382:1159-1165.
   Biofortification of iron content by regulating a NAC transcription factor in maize

The main factor contributing to anemia is iron deficiency. Increasing the iron content of foods is a fundamental, low-cost, and widespread method of improving iron malnutrition. Maize is one of the staple grains and increasing its iron content can alleviate iron deficiency anemia. However, the iron and other nutrients delivery pathways in maize kernels have been an open question. This study used 273 maize inbred lines genotype combined with transcriptome from six extreme materials to identify a candidate gene, ZmNAC78, involved in the regulation of maize kernel iron content. Kernels of transgenic maize overexpressing ZmNAC78 had significantly higher iron content, up to 70.5 mg/kg. The study further dissected the iron delivery pathways in maize kernels. ZmNAC78 was predominantly expressed in the basal endosperm transfer layer (BETL) of maize kernels and activated the expression of the metal ion transporter proteins, ZmYSL11, ZmNRAMP3, and ZmHMA8, in the BETL. Loss of function mutations showed that these metal transporter proteins play important roles in loading of iron into maize kernels, and it is clear that ZmNAC78 and metal transporter proteins together form a molecular switch to control iron delivery into maize kernels. In addition, this study also utilized the polymorphism of ZmNAC78 core promoter sequence to classify maize inbred lines into haplotype 1 with high iron content in kernel and haplotype 2 with low iron content in kernel, and used the haplotype information to breed maize varieties with higher seed iron contents and yields, which will be a feasible option for breeding high-yielding and high-iron maize in the future. In conclusion, this study reveals the iron delivery pathways in maize kernels, and also provided new ideas for dissecting nutrients delivery pathways in wheat and other cereal crops.

Yan, PS et al. 2023. Biofortification of iron content by regulating a NAC transcription factor in maize Science. 382:1159-1165.
   Biofortification of iron content by regulating a NAC transcription factor in maize
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Yuan, Y et al. 2024. Decoding the gene regulatory network of endosperm differentiation in maize Nat Commun. 15:34.
   Decoding the gene regulatory network of endosperm differentiation in maize

The authors analyzed the transcriptome of the developing maize (Zea mays) endosperm during cell differentiation using single-cell transcriptomics. By analyzing 17,022 single cells and the expression of 25,365 genes from 6 to 7 days after pollination, authors identified 12 clusters corresponding to five cell types, and revealed their temporal gene expression patterns. Results revealed heterogeneity of the endosperm composition and complex expression patterns across and withing cell types. Authors combined transcriptomic data with DNA-binding profiles of 161 transcription factors (TF) differentially expressed between cell types to construct a gene regulatory network. This comprehensive network contained 181 regulons, defined as TF with their direct-binding targets, that were mapped to the different cell types to identify specific cell- type regulators. This study generated valuable information for understanding maize endosperm development, a framework that can be applied to other maize tissues, and a web interface to enable researchers to easily navigate the expression and regulatory network atlas of this study (https://www.maize-endosperm.cn).

Early seed developmental stages provide dynamics resource to understand the regulatory function of genes expressed in specific tissue types. Maize endosperm provides an excellent model for developmental and molecular studies considering its size and storage space. The study focused on single cell transcriptomics of maize endosperm during early developmental stage when the cells undergo robust differentiation. A transcriptomic resource of 17,022 single cells was generated between developmental stages 6 to 7 days after pollination (DAP). The authors analyzed the expression of 25,365 genes during the active growth stage of 6 to 7 DAP, that colonizes 12 clusters showing spatial and temporal expression pattern. Endosperm being triploid in nature defines the heterogeneous nature, and so was the expression of the genes within the differentiating cells. Further in the study the authors identified 161 transcription factors (TFs) differentially expressed and analyzed their DNA binding motifs between different cell clusters and constructed a gene regulatory network (GRN), identifying 181 regulons (hub genes) suggesting direct interactions to specific cell types. The regulon map generated in this article corresponding to specific cell clusters in developing endosperm provides a valuable resource to understand the role of important regulators in tissue specific manner during early stages maize endosperm development.

Yuan, Y et al. 2024. Decoding the gene regulatory network of endosperm differentiation in maize Nat Commun. 15:34.
   Decoding the gene regulatory network of endosperm differentiation in maize
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Chen, ZL et al. 2023. Genetic dissection of cis-regulatory control of ZmWUSCHEL1 expression by type-B RESPONSE REGULATORS. Plant Physiol. :doi: 10.1093/plphys/kiad652.
   Genetic dissection of cis-regulatory control of ZmWUSCHEL1 expression by type-B RESPONSE REGULATORS.

Gene expression caused by modification of Cis-regulatory regions is one of the important aspects in evolution and domestication of modern cultivated maize. However, the in plants impact of cis-regulatory control on transcriptional regulation and immediate observed phenotype is challenging. WUSCHEL (WUS) a homeobox transcription factor is known to regulate the shoot meristem biology and young ear development in maize. Hybridization and domestication events have resulted in generation of duplicated gene copies in crops and so in case of maize Barren inflorescence 3 (Bif3) mutant. The mutant Bif3 carries a duplicated copy of ZmWUS1 named ZmWUS-B and the duplicated copy was found to be associated with increased meristem inflorescence. The proximal promoter region of the WUS has 84bp non-coding sequence and is evolutionally conserved. A 69bp fragment of the stretch carries a Type-B RR (Response Regulators) motif (AGATAT). Interestingly this region was found duplicated in a 119bp ZmWUS1-B enhancer region resulting in three repeated AGATAT motifs, flanked by 69-bp fragment. To determine the function of the AGATAT motifs in ZmWUS1-B CRISPR-Cas9 deletion experiments were designed. Multiple editing events generated targeting 69bp conserved nucleotide sequence (CNS) and Type-B RR motifs impact the expression of ZmWUS1-B in consequent ear development. The Cas9 homozygous mutants suggested an expression threshold of ZmWUS1 affecting inflorescence meristem function. To further determine the threshold limit transactivation dual luciferase assay in maize protoplast was done with 444bp region proximal promoter of ZmWUS1. It was found that increased number of AGATAT core motifs result in linear additive effects om ZmWUS1 expression levels. However, the effect tends to weaken and does not produce meaningful impact from distance apart. The ZmWUS1 significantly affects inflorescence development and at the same time applies threshold of buffering capacity for overexpression.

Chen, ZL et al. 2023. Genetic dissection of cis-regulatory control of ZmWUSCHEL1 expression by type-B RESPONSE REGULATORS. Plant Physiol. :doi: 10.1093/plphys/kiad652.
   Genetic dissection of cis-regulatory control of ZmWUSCHEL1 expression by type-B RESPONSE REGULATORS.
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Lisa Thoenen et al. 2023. Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome. Proc Natl Acad Sci, USA. 120:e2310134120.
   Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome.

The effect of microbes in determining the plant health and nutrient acquisition from soil is well known concept. However, the signaling mechanism responsible for establishing the interaction of microbes with plant roots especially maize are less understood. Various studies have shown that maize roots secrete benzoxazinoids (BXs), a bioactive metabolite in the root exudates which could structure the maize root microbiome. Here in this study Thoenen et al. (2023), reveal that one of the major determinants of root conization is tolerance of microbes to plant specialized metabolites. Authors established a representative collection of maize root bacteria (MRB) and tested their tolerance against BXs. There experiment showed the compound- and strain dependent inhibition of bacterial growth. They also showed that tolerance to BXs compounds depend on cell wall structure of bacterial strain with Gram-positive MRB isolates were more tolerant compared to the gram-negative ones. This study alludes to specific and important role of BXs in controlling the root colonization and could have role in deciding the positive and negative associations. In conclusion, this study can be helpful in designing of microbial composition suitable for a specific host like maize or other species for enhancing the nutrient utilization.

Lisa Thoenen et al. 2023. Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome. Proc Natl Acad Sci, USA. 120:e2310134120.
   Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome.
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Yang, N et al. 2023. Two teosintes made modern maize. Science 282: 6674
   Two teosintes made modern maize

Structured Abstract: INTRODUCTION AND RATIONALE: The drastic morphological differences between maize and its wild relatives gave rise to more than a century of debate about its origins. Today, the most widely accepted model is also the simplest—maize was domesticated once from the wild annual grass Zea mays ssp. parviglumis in the lowlands of southwest Mexico. More recently, however, genomic surveys of traditional maize varieties in both Mexico and South America have identified evidence for gene flow from a second wild relative, Zea mays ssp. mexicana, a weedy annual grass adapted to the central Mexican highlands. These results, combined with long-standing archaeological evidence of hybridization, challenge the sufficiency of a simple model of a single origin. RESULTS: To elucidate the genetic contributions of Zea mays ssp. mexicana to maize, we analyzed >1000 wild and domesticated genomes, including 338 newly sequenced traditional varieties. We found ubiquitous evidence for admixture between maize and Zea mays ssp. mexicana, including in ancient samples from North and South America, diverse traditional varieties, and even modern inbred lines. These results are mirrored in a genotyping survey of >5000 traditional varieties representing maize diversity across the Americas. The only maize sample surveyed that lacks strong evidence for admixture with Zea mays ssp. mexicana is a single ancient South American sample N16, dating to ~5500 years before present. We next fit graphs of population history to our data, revealing multiple admixture events in the history of modern maize. On the basis of these results, we propose a new model of maize origins, which posits that, some 4000 years after domestication, maize hybridized with Zea mays ssp. mexicana in the highlands of central Mexico. The resulting admixed maize then spread across the Americas, replacing or hybridizing with preexisting populations. The timing of this secondary dispersal is roughly coincident with archaeological data showing a transition to a staple maize diet in regions across Mesoamerica. We then explored variation in ancestry along the maize genome. We found that 15 to 25% of the genome could be attributed to Zea mays ssp. mexicana ancestry. We identified regions in which Zea mays ssp. mexicana alleles had reached high frequency in maize, presumably as a result of positive selection. We investigated one of these adaptive introgressions in more detail, using CRISPR-Cas9 knockout mutants and overexpression lines to demonstrate the role of the circadian clock gene ZmPRR37a in determining flowering time under long-day conditions. Our results suggest that introgression at this locus may have facilitated the adaptation of maize to higher latitudes. Finally, we explored the contributions of Zea mays ssp. mexicana alleles to phenotypic variation in maize. Admixture mapping identified at least 25 loci in modern inbred lines where highland teosinte ancestry associates with phenotypes of agronomic importance, from oil content to kernel size and disease resistance, as well as a large effect locus associated with cob diameter in traditional maize varieties. We then modeled the additive genetic variance of each phenotype, allowing us to estimate that Zea mays ssp. mexicana admixture explained a meaningful proportion of the additive genetic variation for many traits, including 25% of the variation for the number of kernels per row and nearly 50% of some disease phenotypes. CONCLUSION: Our extensive population and quantitative genetic analysis of domesticated maize and its wild relatives uncovered a substantial role for two different wild taxa in making modern maize. We propose a new model for the origin of maize that can explain both genetic and archaeological data, and we show how variation in Zea mays ssp. mexicana is a key component of maize diversity, both at individual loci and for genetic variation underlying agronomic traits. Our model raises a number of questions about how and why a secondary spread of maize may have occurred, but we speculate that the timing of admixture suggests a possible direct role for hybridization between maize and Zea mays ssp. mexicana in improving early domesticated forms of maize, helping to transform it into the staple crop we know today. Editor’s summary: Domestication of plants and animals is often characterized by selection for specific traits interspersed with introduction of new desirable traits from wild relatives. Yang et al. examined genetic data from more than 1000 varieties of maize and related species to clarify the complex origins of this agricultural staple. They found evidence that after initial domestication, introgression from a relative of domesticated maize, Zea mays ssp. mexicana, occurred in the highlands of Mexico before propagating across Central America. Alleles from this wild relative affect photoperiodicity and flowering time, which suggests that traits from Zea mays ssp. mexicana may have been beneficial during domestication. These results demonstrate the importance of broad sampling in elucidating the history of domesticates. —Corinne Simonti

See also: https://www.science.org/content/article/scientists-thought-they-understood-maizes-origins-they-were-missing-something-big

This paper proposes a new model of the origin of maize, and discovers two completely different species of Zea mays ssp. Parviglumis and Zea mays ssp. Mexicana are the ancestors of modern maize, revising the hypothesis that maize originated from Zea mays ssp. Parviglumis. (Qiang Ning, Editorial Board Comment December 2023)

Hypotheses about the origin of maize have centered on its domestication from the lowland teosinte Zea mays spp. parviglumis, however this model fails to incorporate evidence that suggests a more complex origin. Using 338 newly sequenced traditional Mexican maize varieties, archaeological samples, modern US varieties and traditional Chinese varieties, the authors found evidence of admixture with the highland Zea mays spp. mexicana. Variation in the mexicana admixture may have resulted in 1) the reduction of genetic load and 2) adaptation to higher latitudes. Admixture from teosinte also contributes to phenotypic variation in agronomic traits such as cold tolerance, cob size, and flowering time in modern maize. Altogether these data suggest a new model where introgression from mexicana contributed to a secondary spread of maize after its initial domestication. (Aimee Uyehara, Editorial Board Comment December 2023 and January 2024)

Understanding the domestication of maize is of great interest for the scientific community as it provides guidance for the introgression of new diversity and key adaptation traits into cultivated maize. It was believed maize domestication occurred from the annual grass zea mays spp. Parviglumis in the lowlands of southwest Mexico; however, evidence has raised suggesting gene flow from a second wild relative zea mays spp. mexicana, a weedy annual grass from the central Mexican high lands. This in combination with archeological evidence suggest a single origin of domesticated maize might not be possible. For the above-mentioned reasons, the authors analyzed a large number of genomes from wild and domesticated (>1000) maize, as well as maize varieties (>5000) representing the diversity across the Americas to elucidate the contribution of mexicana to maize domestication. Authors observed strong evidence of admixture with 15-25% of maize genome originating from mexicana. Suggesting domesticated maize hybridized with mexicana 4000 years after domestication and spread across America replacing or hybridizing with preexisting populations. In addition, they demonstrated the role of the circadian clock gene ZmPRR37a in determining flowering time under long-day conditions via CRISPR-Cas9 knockout and overexpression experiments. The introgression of this locus from mexicana likely facilitated adaptation of maize to higher latitudes. Mexicana also contributed other alleles associated with cob diameter, oil content, kernel size, and disease resistance. This new evidence and model suggest a key role of the hybridization with mexicana in the domestication of maize and highlight key adaptation loci. (Diana Escamilla Sanchez, Editorial Board Comment January 2024)

Yang, N et al. 2023. Two teosintes made modern maize. Science 282: 6674
   Two teosintes made modern maize
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Yin, P et al. 2023. Cytokinin signaling promotes salt tolerance by modulating shoot chloride exclusion in maize. Molecular Plant.
   Cytokinin signaling promotes salt tolerance by modulating shoot chloride exclusion in maize.

Ion toxicity caused by soil salinization is one of the major environmental factors that harms crop yield as well as quality. A list of genes regulating Na+ uptake and transport have been cloned from different crops, but the molecular mechanism and genetic basis of the regulation of Cl- uptake and transport are still unclear. In this study, an A-type response regulator, ZmRR1, was identified from transgenic maize lines tested for salt tolerance, which negatively regulates maize salt tolerance by negatively regulating the cytokinin signaling pathway. On the basis of this result, the molecular mechanism by which cytokinin promotes salt tolerance in maize through the regulation of Cl- transport was elucidated. Under salt stress, ZmRR1 protein levels decreased and its inhibition of ZmHP2, a positive regulator of cytokinin signaling, was deregulated, and then ZmHP2-mediated cytokinin signaling up-regulated the expression of ZmMATE29 (encoding a vesicle-localized protein that can translocate Cl-), which, in turn, promotes salt tolerance in maize by compartmentalizing Cl- into vacuoles of root cortex cells in order to reduce the transport of Cl- from roots to the shoots. In addition, this study also analyzed the natural variation that affect ZmRR1 function through GWAS of 311 maize inbred lines seedling biomass phenotypes and candidate gene association analysis, and found that a non-synonymous SNP (SNP307-T) enhanced the interaction between ZmRR1 and ZmHP2. As a result, the ZmHP2-dependent up-regulation of ZmMATE29 expression under salt stress is blocked, resulting in excessive Cl- being transported from the roots to the shoots, making the SNP307-T inbred line more sensitive to salt stress than the SNP307-C inbred line. This locus provides a new target site for the improvement of salt tolerance in maize.

Yin, P et al. 2023. Cytokinin signaling promotes salt tolerance by modulating shoot chloride exclusion in maize. Molecular Plant.
   Cytokinin signaling promotes salt tolerance by modulating shoot chloride exclusion in maize.
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Grzybowski, M et al. 2023. A Common Resequencing-Based Genetic Marker Dataset for Global Maize Diversity. Plant J. :doi: 10.1111/tpj.16123.
   A Common Resequencing-Based Genetic Marker Dataset for Global Maize Diversity.

Maize populations exhibit great genetic and phenotypic diversity. Exploring the association between phenotypic and genomic variations by genome-wide association studies and/or QTL mapping is a central method in identifying genetic elements controlling phenotypes of interests. The fast advancement in genome sequencing technology enables frequent resequencing of the same maize samples to gain better mapping resolution and higher accuracy. However, these resequencing datasets are produced by different projects that employ different analytical pipelines with different reference genome assemblies and consistently filter for minor allele frequency within the study population. This constrains the potential of performing meta-analysis of these datasets (i.e., reuse and remix data) to address new biological questions. Grzybowski et al. integrated 1515 resequencing datasets (including 1276 previously published and 239 self-generated) into a single unified marker set including 366M segregating single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Moreover, this market set contains 46 million high-confidence variants scored across crop wild relatives, landraces as well as tropical and temperate lines from different breeding eras. Grzybowski et al. has demonstrated that the new variant set increased the power to identify known causal flowering-time genes, and increased the potential to track changes in the frequency of functionally distinct alleles across the global distribution of modern maize. The 46 M high-confidence genome variants are currently available in maizeGDB.

Grzybowski, M et al. 2023. A Common Resequencing-Based Genetic Marker Dataset for Global Maize Diversity. Plant J. :doi: 10.1111/tpj.16123.
   A Common Resequencing-Based Genetic Marker Dataset for Global Maize Diversity.
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Xing, JP et al. 2023. Mining genic resources regulating nitrogen-use efficiency based on integrative biological analyses and their breeding applications in maize and other crops. Plant J. :doi: 10.1111/tpj.16550.
   Mining genic resources regulating nitrogen-use efficiency based on integrative biological analyses and their breeding applications in maize and other crops.

Maize, being the primary crop in terms of overall production, heavily relies on substantial quantities of nitrogen fertilizer input to achieve a high yield. However, this practice leads to low nitrogen-use efficiency (NUE) and worsens the risks to agricultural and environmental systems, food security, and human health. This work aims to investigate the genetic resources that regulate NUE in maize and other crops by utilizing integrated quantitative trait loci (QTL) and quantitative trait nucleotide (QTN) analysis, as well as multi-omics data mining. A thorough bibliometric analysis was initially conducted, encompassing six distinct categories: controlling variation, elevated CO2, genomic resource, N availability, glutamine synthetase, and environment interaction. The purpose of this analysis was to observe the overall status, patterns of innovation, and overall trend toward improving NUE in crops. A total of 555 QTLs and 728 QTNs were discovered, exhibiting associations with attributes linked to NUE. Among these, 12 genetic loci exhibited overlapping between QTL and QTN hotspots. Using transcriptome analysis, researcher further discovered genes associated with phytohormones, such as ZmCKX10 (which encodes cytokinin dehydrogenase), ZmIAA20 (gene responsive to auxin), and ZmCIPK44 (which responds to abiotic stresses through an ABA-dependent pathway). These genes likely have significant functions in the response to nitrogen stress. Additionally, they observed that ZmGBSS1b, ZmHB41, and ZmXYL4 were primarily impacted by low nitrogen stress, and they likely have crucial functions in carbohydrate metabolism and the transportation of carbohydrate/nitrogen compounds. Glutamate, glutamine, aspartate, and asparagine are the initial and intermediate products of nitrogen assimilation, and their levels were significantly reduced by nitrogen stress, ultimately impeding plant growth and yield. In conclusion, the widespread implementation of these methods is anticipated to enhance crop NUE and promote long-term agricultural sustainability.

Xing, JP et al. 2023. Mining genic resources regulating nitrogen-use efficiency based on integrative biological analyses and their breeding applications in maize and other crops. Plant J. :doi: 10.1111/tpj.16550.
   Mining genic resources regulating nitrogen-use efficiency based on integrative biological analyses and their breeding applications in maize and other crops.
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Fu, YX et al. 2023. Spatial transcriptomics uncover sucrose post-phloem transport during maize kernel development Nat Commun. 14:7191.
   Spatial transcriptomics uncover sucrose post-phloem transport during maize kernel development

This study utilized spatial transcriptomics to investigate gene expression patterns during maize kernel development. Tissue sections from kernels at three filling stages (12, 18 and 24 DAP) were analyzed using the 10x Genomics Visium platform. Over 26,000 genes were found to be expressed across the sections. Computational analysis identified 11 distinct cell populations within the kernels based on gene expression profiles. These included cell types in maternal tissues, embryo and endosperm. Further analysis defined 332 molecular marker genes that could be used to precisely localize each cell type. Gene ontology analysis revealed specific biological processes enriched in different cell populations, such as starch and protein biosynthesis in endosperm and lipid storage in embryo. Validation experiments confirmed the accuracy of the identified marker genes. The study also constructed a co-expression network to analyze relationships between gene modules and cell populations. Three major functional regions were identified - storage accumulation, offspring development and maternal-filial interface. Key genes involved in sucrose transport and storage of starch, protein and oil were mined from the differential expression analysis. Notably, genes specifically expressed in endosperm-BETL and endosperm-EAS suggested their important roles in nutrient transport. Genetic analysis of ZmSUT1 and ZmSUT7 further demonstrated their essential functions in grain filling. This is the first study to characterize genome-wide spatial gene expression patterns during maize kernel development using a high-throughput approach. The comprehensive single-cell atlas and electronic RNA maps generated provide a valuable resource for exploring functional genes regulating important agronomic traits in maize.

Fu, YX et al. 2023. Spatial transcriptomics uncover sucrose post-phloem transport during maize kernel development Nat Commun. 14:7191.
   Spatial transcriptomics uncover sucrose post-phloem transport during maize kernel development
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Chen Chen et al. 2023. The role of media in influencing students’ STEM career interest Int J STEM Educ. 10
   The role of media in influencing students’ STEM career interest

Digital media has become part of modern life and significantly impacts decisions and perceptions. In this paper, the authors describe the role of media in developing STEM career interests among pre-college students. The study involved about 15,752 first-year US college and university students through retrospective reporting of their interaction with STEM-related media at high school. The authors employed a theoretical framework combining Cultivation Theory, Social Cognitive Theory, and the Expectancy-Value Theory to test the direct and indirect effects of high school stem-related media on STEM career interests in college. They report the positive association of STEM-related media with STEM career interest and evidence of the indirect impact of STEM media on STEM career interest, especially on STEM identity and perceived personal career outcomes. The paper alludes to the importance of the early inception of STEM career interests in students and suggests the need for timely fostering of these interests in students' lives.

Chen Chen et al. 2023. The role of media in influencing students’ STEM career interest Int J STEM Educ. 10
   The role of media in influencing students’ STEM career interest
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Yang, N et al. 2023. Two teosintes made modern maize. Science 282: 6674
   Two teosintes made modern maize

Structured Abstract: INTRODUCTION AND RATIONALE: The drastic morphological differences between maize and its wild relatives gave rise to more than a century of debate about its origins. Today, the most widely accepted model is also the simplest—maize was domesticated once from the wild annual grass Zea mays ssp. parviglumis in the lowlands of southwest Mexico. More recently, however, genomic surveys of traditional maize varieties in both Mexico and South America have identified evidence for gene flow from a second wild relative, Zea mays ssp. mexicana, a weedy annual grass adapted to the central Mexican highlands. These results, combined with long-standing archaeological evidence of hybridization, challenge the sufficiency of a simple model of a single origin. RESULTS: To elucidate the genetic contributions of Zea mays ssp. mexicana to maize, we analyzed >1000 wild and domesticated genomes, including 338 newly sequenced traditional varieties. We found ubiquitous evidence for admixture between maize and Zea mays ssp. mexicana, including in ancient samples from North and South America, diverse traditional varieties, and even modern inbred lines. These results are mirrored in a genotyping survey of >5000 traditional varieties representing maize diversity across the Americas. The only maize sample surveyed that lacks strong evidence for admixture with Zea mays ssp. mexicana is a single ancient South American sample N16, dating to ~5500 years before present. We next fit graphs of population history to our data, revealing multiple admixture events in the history of modern maize. On the basis of these results, we propose a new model of maize origins, which posits that, some 4000 years after domestication, maize hybridized with Zea mays ssp. mexicana in the highlands of central Mexico. The resulting admixed maize then spread across the Americas, replacing or hybridizing with preexisting populations. The timing of this secondary dispersal is roughly coincident with archaeological data showing a transition to a staple maize diet in regions across Mesoamerica. We then explored variation in ancestry along the maize genome. We found that 15 to 25% of the genome could be attributed to Zea mays ssp. mexicana ancestry. We identified regions in which Zea mays ssp. mexicana alleles had reached high frequency in maize, presumably as a result of positive selection. We investigated one of these adaptive introgressions in more detail, using CRISPR-Cas9 knockout mutants and overexpression lines to demonstrate the role of the circadian clock gene ZmPRR37a in determining flowering time under long-day conditions. Our results suggest that introgression at this locus may have facilitated the adaptation of maize to higher latitudes. Finally, we explored the contributions of Zea mays ssp. mexicana alleles to phenotypic variation in maize. Admixture mapping identified at least 25 loci in modern inbred lines where highland teosinte ancestry associates with phenotypes of agronomic importance, from oil content to kernel size and disease resistance, as well as a large effect locus associated with cob diameter in traditional maize varieties. We then modeled the additive genetic variance of each phenotype, allowing us to estimate that Zea mays ssp. mexicana admixture explained a meaningful proportion of the additive genetic variation for many traits, including 25% of the variation for the number of kernels per row and nearly 50% of some disease phenotypes. CONCLUSION: Our extensive population and quantitative genetic analysis of domesticated maize and its wild relatives uncovered a substantial role for two different wild taxa in making modern maize. We propose a new model for the origin of maize that can explain both genetic and archaeological data, and we show how variation in Zea mays ssp. mexicana is a key component of maize diversity, both at individual loci and for genetic variation underlying agronomic traits. Our model raises a number of questions about how and why a secondary spread of maize may have occurred, but we speculate that the timing of admixture suggests a possible direct role for hybridization between maize and Zea mays ssp. mexicana in improving early domesticated forms of maize, helping to transform it into the staple crop we know today. Editor’s summary: Domestication of plants and animals is often characterized by selection for specific traits interspersed with introduction of new desirable traits from wild relatives. Yang et al. examined genetic data from more than 1000 varieties of maize and related species to clarify the complex origins of this agricultural staple. They found evidence that after initial domestication, introgression from a relative of domesticated maize, Zea mays ssp. mexicana, occurred in the highlands of Mexico before propagating across Central America. Alleles from this wild relative affect photoperiodicity and flowering time, which suggests that traits from Zea mays ssp. mexicana may have been beneficial during domestication. These results demonstrate the importance of broad sampling in elucidating the history of domesticates. —Corinne Simonti

See also: https://www.science.org/content/article/scientists-thought-they-understood-maizes-origins-they-were-missing-something-big

This paper proposes a new model of the origin of maize, and discovers two completely different species of Zea mays ssp. Parviglumis and Zea mays ssp. Mexicana are the ancestors of modern maize, revising the hypothesis that maize originated from Zea mays ssp. Parviglumis. (Qiang Ning, Editorial Board Comment December 2023)

Hypotheses about the origin of maize have centered on its domestication from the lowland teosinte Zea mays spp. parviglumis, however this model fails to incorporate evidence that suggests a more complex origin. Using 338 newly sequenced traditional Mexican maize varieties, archaeological samples, modern US varieties and traditional Chinese varieties, the authors found evidence of admixture with the highland Zea mays spp. mexicana. Variation in the mexicana admixture may have resulted in 1) the reduction of genetic load and 2) adaptation to higher latitudes. Admixture from teosinte also contributes to phenotypic variation in agronomic traits such as cold tolerance, cob size, and flowering time in modern maize. Altogether these data suggest a new model where introgression from mexicana contributed to a secondary spread of maize after its initial domestication. (Aimee Uyehara, Editorial Board Comment December 2023 and January 2024)

Understanding the domestication of maize is of great interest for the scientific community as it provides guidance for the introgression of new diversity and key adaptation traits into cultivated maize. It was believed maize domestication occurred from the annual grass zea mays spp. Parviglumis in the lowlands of southwest Mexico; however, evidence has raised suggesting gene flow from a second wild relative zea mays spp. mexicana, a weedy annual grass from the central Mexican high lands. This in combination with archeological evidence suggest a single origin of domesticated maize might not be possible. For the above-mentioned reasons, the authors analyzed a large number of genomes from wild and domesticated (>1000) maize, as well as maize varieties (>5000) representing the diversity across the Americas to elucidate the contribution of mexicana to maize domestication. Authors observed strong evidence of admixture with 15-25% of maize genome originating from mexicana. Suggesting domesticated maize hybridized with mexicana 4000 years after domestication and spread across America replacing or hybridizing with preexisting populations. In addition, they demonstrated the role of the circadian clock gene ZmPRR37a in determining flowering time under long-day conditions via CRISPR-Cas9 knockout and overexpression experiments. The introgression of this locus from mexicana likely facilitated adaptation of maize to higher latitudes. Mexicana also contributed other alleles associated with cob diameter, oil content, kernel size, and disease resistance. This new evidence and model suggest a key role of the hybridization with mexicana in the domestication of maize and highlight key adaptation loci. (Diana Escamilla Sanchez, Editorial Board Comment January 2024)

Yang, N et al. 2023. Two teosintes made modern maize. Science 282: 6674
   Two teosintes made modern maize
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Shen, XM et al. 2023. Dynamic transcriptome landscape of developing maize ear Plant J. :doi: 10.1111/tpj.16457.
   Dynamic transcriptome landscape of developing maize ear

Seed number and harvesting ability in maize (Zea mays L.) are primarily determined by the architecture of female inflorescence, namely the ear. Therefore, ear morphogenesis contributes to grain yield and as such is one of the key target traits during maize breeding. However, the molecular networks of this highly dynamic and complex grain-bearing inflorescence remain largely unclear. As a first step toward characterizing these networks, authors performed a high-spatio-temporal-resolution investigation of transcriptomes using 130 ear samples collected from developing ears with length from 0.1 mm to 19.0 cm. Comparisons of these mRNA populations indicated that these spatio-temporal transcriptomes were clearly separated into four distinct stages stages I, II, III, and IV. A total of 23 793 genes including 1513 transcription factors (TFs) were identified in the investigated developing ears. During the stage I of ear morphogenesis, 425 genes were predicted to be involved in a co-expression network established by eight hub TFs. Moreover, 9714 ear-specific genes were identified in the seven kinds of meristems. Additionally, 527 genes including 59 TFs were identified as especially expressed in ear and displayed high temporal specificity. These results provide a high-resolution atlas of gene activity during ear development and help to unravel the regulatory modules associated with the differentiation of the ear in maize.

Shen, XM et al. 2023. Dynamic transcriptome landscape of developing maize ear Plant J. :doi: 10.1111/tpj.16457.
   Dynamic transcriptome landscape of developing maize ear
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E. Jakku et al. 2023. Disruption disrupted? Reflecting on the relationship between responsible innovation and digital agriculture research and development at multiple levels in Australia and Aotearoa New Zealand Agricultural Systems. 204:103555.
   Disruption disrupted? Reflecting on the relationship between responsible innovation and digital agriculture research and development at multiple levels in Australia and Aotearoa New Zealand

Technology development in agriculture is growing at a staggering pace. Digital tools and technologies, contributing to the ‘smart farm’ of the future, represent a large part of that growth. Historically, new technologies have not been broadly accessible and cause disruption that can be hard to mitigate, especially to those who could benefit from or are affected by them the most. Responsible innovation scholarship aims to foster collective stewardship of research and innovation so that technology development is proactive in addressing social and ethical issues and responsibilities involved. In this paper, research teams at two public research universities, one in Australia and the other in Aotearoa New Zealand combine their research findings on the sociological dimensions of digital agriculture programs, reflect critically on their own experience, and provide a summary of four workshops in which participants considered what is needed to implement responsible research innovation. The authors frame their analysis around two questions: Who is responsible for being responsible? and What can these individuals and groups teach us about the ‘responsibilization’ of digital agriculture at the national scale and broader? The authors address these questions by examining existing structures such as the co-design and co-production of new technologies, the components of program/project design and development cycles, and organizational culture within research institutions and funding agencies. This reflective study provides much food for thought and practical approaches for the intentional incorporation of responsible technology innovation, especially for leaders at the project, program, institution, and funding agency levels.

E. Jakku et al. 2023. Disruption disrupted? Reflecting on the relationship between responsible innovation and digital agriculture research and development at multiple levels in Australia and Aotearoa New Zealand Agricultural Systems. 204:103555.
   Disruption disrupted? Reflecting on the relationship between responsible innovation and digital agriculture research and development at multiple levels in Australia and Aotearoa New Zealand
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Wesley Neher et al. 2023. The maize preligule band is subdivided into distinct domains with contrasting cellular properties prior to ligule outgrowth. Development. :doi: 10.1242/dev.201608.
   The maize preligule band is subdivided into distinct domains with contrasting cellular properties prior to ligule outgrowth.

How do different parts of the leaf arise? This paper looks at the role of cellular properties, i.e. cell division patterns, cell geometry, and cell wall rigidity, in defining boundary domains using the development of a specialized structure called the ligule that separates the leaf sheath and blade. During ligule development, cell divisions reorient to become periclinal, where the division plane is parallel to the tissue surface, and differentially thicken such that the sheath and proximal ligule region are thicker than blade cells. Cells in the ligule region also become less rigid, potentially enabling cell expansion and ligule outgrowth. Auxin may be involved as localization of a reporter for auxin efflux, PIN1a-YFP, labels the ligule region and narrows during ligule development. However, auxin responses as reported through the synthetic DR5 reporter were not elevated early in ligule development. This characterization of ligule development is an important step in understanding the processes that coordinate the specification of different parts of the leaf.

Wesley Neher et al. 2023. The maize preligule band is subdivided into distinct domains with contrasting cellular properties prior to ligule outgrowth. Development. :doi: 10.1242/dev.201608.
   The maize preligule band is subdivided into distinct domains with contrasting cellular properties prior to ligule outgrowth.
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Zhu, WC et al. 2023. A translatome-transcriptome multi-omics gene regulatory network reveals the complicated functional landscape of maize Genome Biol. 24:60.
   A translatome-transcriptome multi-omics gene regulatory network reveals the complicated functional landscape of maize

Although massive amounts of transcriptomic data have been generated in maize, an atlas at the translatomic level is still lacking, and inter-omics regulatory networks between the translatome and transcriptome have not been assembled in eukaryotes. Authors collect spatio-temporal translatome and transcriptome data and systematically explore the landscape of gene transcription and translation across 33 tissues or developmental stages of maize. Using this comprehensive transcriptome and translatome atlas, they construct a multi-omics gene regulatory networks (GRN) integrating mRNAs and translated mRNAs, demonstrating that translatome-related GRNs outperform GRNs solely using transcriptomic data and inter-omics GRNs outperform intra-omics GRNs in most cases. With the aid of the multi-omics GRN, they reconcile some known regulatory networks, and identify a novel transcription factor, ZmGRF6, which is associated with growth. Furthermore, they also characterize a function related to drought response for the classic transcription factor ZmMYB31. Together, these findings provide insights into spatio-temporal changes across maize development at both the transcriptome and translatome levels. Multi-omics GRNs represent a useful resource for dissection of the regulatory mechanisms underlying phenotypic variation.

Zhu, WC et al. 2023. A translatome-transcriptome multi-omics gene regulatory network reveals the complicated functional landscape of maize Genome Biol. 24:60.
   A translatome-transcriptome multi-omics gene regulatory network reveals the complicated functional landscape of maize
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Gregory M Walton et al. 2023. Where and with whom does a brief social-belonging intervention promote progress in college? 380:499-505.
   Where and with whom does a brief social-belonging intervention promote progress in college?

Affordable large-scale interventions could be powerful tools for sustained support and promotion of diversity in STEM. In this paper, the authors discuss a large-scale intervention to strengthen diversity through supporting progress at college from an intervention for social belonging support among students. The study utilized a short (30-minute) online module administered intervention involving several participants, including 14,154 disadvantaged students (belonging to ethnic minorities or classified as first-generation students, except for White and Asian continuing-generation students). The results indicated increased college progression through the first year following the intervention and demonstrated the dependence of the intervention's success on the availability of required support in the form of opportunities to belong. The described opportunities to belong included communication platforms, residential programming avenues, dedicated institutions and institutional programs, pedagogy, increased representation of diverse groups, and opportunities for student-student and student-faculty interactions. This paper highlights how and what is needed for simple, sustainable interventions in promoting diversity in STEM.

Gregory M Walton et al. 2023. Where and with whom does a brief social-belonging intervention promote progress in college? 380:499-505.
   Where and with whom does a brief social-belonging intervention promote progress in college?
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Xi Wang et al. 2023. QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize Nat Commun. 14:5232.
   QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize

In this study, Wang et al. developed a multi-omics data-based technique, namely QTG-Miner, for large-scale and rapid cloning of quantitative trait genes (QTGs) in maize. This strategy incorporates three steps. Step 1: QTL mapping for the target trait. Step 2: RNA-seq analysis to detect the differentially expressed genes and sequence variants among a selection of individuals that show the greatest contrast within the QTLs identified step 1, but have similar genomic context outside the QTLs. Step 3: Candidate gene mining that uses machine learning-based methods to compare the genes located within the selected QTLs versus known trait-associated genes and/or verified trait-unassociated genes. Using QTG-Miner, followed by functional validation with EMS and CRISPR-Cas9, Wang et al. cloned and verified the functional association of seven genes underlying seven tassel branch number QTLs. Moreover, the seven verified QTLs have effects ranging from 4.6 to 14.4%, indicating that QTG-Miner can effectively identify candidate genes from both major-effect and minor-effect QTLs. In addition, a comprehensive molecular network underlying tassel branch number was constructed based on the QTG-Miner results, and the resultant network contained 12 biological pathways. Selection signatures are significantly enriched in multiple biological pathways between female heterotic groups and male heterotic groups.

Xi Wang et al. 2023. QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize Nat Commun. 14:5232.
   QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize
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Erwang Chen et al. 2023. The transcription factors ZmNAC128 and ZmNAC130 coordinate with Opaque2 to promote endosperm filling in maize Plant Cell. :doi: 10.1093/plcell/koad215.
   The transcription factors ZmNAC128 and ZmNAC130 coordinate with Opaque2 to promote endosperm filling in maize

The endosperm of maize functions as the primary storage site for both starch and proteins (mainly zein), constituting approximately 90% of the total kernel’s weight. The developmental process of the endosperm holds paramount importance. High-resolution spatiotemporal transcriptome analyses have identified several key genes, including sugar transporters and the Opaque2 (O2) transcription factor (TF). These genes play a direct role in regulating the expression of carbohydrate- and protein-related genes in maize. In a previous study, ZmNAC128 and ZmNAC130 were identified as crucial coordinators for the synchronized synthesis of zeins and starch. However, the intricate gene regulatory network governing their function remained largely unexplored. The present study aims to elucidate the significance of ZmNAC128 and ZmNAC130 in endosperm filling. The gene-edited double mutant zmnac128 zmnac130 together with RNA-seq analysis exhibits a poorly filled kernel phenotype, with reduced expression of many genes involved in zein and starch biosynthesis as well as O2 gene. Further investigation, employing DAP-seq combined with CHIP-seq, conclusively demonstrated that ZmNAC128 and ZmNAC130 are direct regulators of three (16-, 27-, and 50-kD) γ-zein genes and six pivotal genes related to starch metabolism (Bt2, Zpu1, GBSS1, SS1, SSIIa, and Sus1). They also discovered that the reduced expression of O2 was caused by physical interactions between these three TFs and that the combined effect of these regulates endosperm filling, zein, sugar, starch synthesis, and nutrient uptake in maize.

Erwang Chen et al. 2023. The transcription factors ZmNAC128 and ZmNAC130 coordinate with Opaque2 to promote endosperm filling in maize Plant Cell. :doi: 10.1093/plcell/koad215.
   The transcription factors ZmNAC128 and ZmNAC130 coordinate with Opaque2 to promote endosperm filling in maize
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Huang, YC et al. 2022. THP9 enhances seed protein content and nitrogen-use efficiency in maize Nature. :doi: 10.1038/s41586-022-05441-2.
   THP9 enhances seed protein content and nitrogen-use efficiency in maize

The domestication of teosinte, the wild ancestor of maize, into modern maize focused mostly on yield and starch content, while protein content and flavor received less consideration. Variation in seed protein content (α-zein) and asparagine level reveals that the loci that control seed protein content are genetically variable between teosinte, Zea mays subsp. parviglumis (Ames accession 21814) and modern maize inbreds (B73). In this paper, the researchers have created a high-quality teosinte haplotype assembly for comparing α-zein loci in Ames 21814 and other inbreds and decode the haplotype information of a single F1 plant using a trio-binning approach. On chromosome 9, they identified TEOSINTE HIGH PROTEIN 9 (THP9) as a key quantitative trait locus for high-protein content (α-zein). Fine mapping of THP9 revealed three genes (Zm00001d047732, Zm00001d047736 and Zm00001d047737). Zm00001d047736, which corresponds to Teo09G002926, encodes an asparagine synthetase 4 (ASN4) enzyme that is abundantly expressed in teosinte with an intact ASN4 gene but not in the B73 inbred, in which a loss in the tenth intron of THP9-B73 results in improper splicing of THP9-B73 transcripts. Transgenic expression of THP9-teosinte in B73 resulted in a significant increase in seed protein content. Introgression of THP9-teosinte into current maize inbreds and hybrids substantially boosted the accumulation of free amino acids, particularly asparagine, throughout the plant and increased the seed protein content without affecting yield. THP9-teosinte appears to boost nitrogen-use efficiency, which is crucial for fostering high yields in low-nitrogen environments. (Anuradha Singh, November 2022)

As early as 9,000 years ago, the ancestors of humans in the Americas began to domesticate maize, gradually transforming a wild maize called "teosinte" into an edible crop. During the domestication process, the starch content and yield of maize continuously increased, making it one of the most widely used feed today. However, at the same time, this domestication process also sacrificed some of the excellent qualities of maize. Surprisingly, the protein content of the ancestral maize seeds far exceeds that of modern maize. However, the mechanism behind the high protein content in wild maize seeds has been a long-standing unresolved century-old problem, and the key genes that control the total protein content of maize and efficient nitrogen utilization have not been found. The research team first successfully assembled a heterozygous and complex wild maize haploid genome through the combination of third-generation sequencing technology and three-dimensional genomics, which was used for the positioning and cloning of high protein genes in wild maize. Through map-based cloning, a major quantitative trait locus for high protein content, TEOSINTE HIGH PROTEIN 9 (THP9), was identified on chromosome 9. This gene encodes asparagine synthetase 4 (ASN4), and ASN is the center of nitrogen metabolism, responsible for the synthesis of asparagine. Asparagine plays a central role in nitrogen cycling and acts as a nitrogen donor in intermolecular transfer reactions of amino groups. Therefore, the level of asparagine in plants is closely related to seed protein content. The study found that the excellent gene THP9-T in wild maize was significantly upregulated, while the mutated form THP9-B, in B73 and some maize inbred lines, resulted in lower expression of ASN4. After introducing the THP9-T gene into modern maize inbred lines and hybrids, the accumulation of free amino acids, especially asparagine, in maize plants was greatly increased, and the seed protein content was also increased without affecting the yield. THP9-T can improve nitrogen utilization efficiency and is of great significance for promoting high yield under low nitrogen conditions. (Jun Yan, September 2023)

Huang, YC et al. 2022. THP9 enhances seed protein content and nitrogen-use efficiency in maize Nature. :doi: 10.1038/s41586-022-05441-2.
   THP9 enhances seed protein content and nitrogen-use efficiency in maize
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Li, H et al. 2023. IQ domain-containing protein ZmIQD27 modulates water transport in maize. Plant Physiol. :doi: 10.1093/plphys/kiad390.
   IQ domain-containing protein ZmIQD27 modulates water transport in maize.

The primary objective of this investigation was to identify drought tolerance mechanisms in Zea mays. Li et al. (2023) commence this investigation by screening maize mutants induced by EMS for drought-related phenotypes. They identified line iqd27-1, which exhibited drought-sensitive phenotypes and was controlled by the ZmIQD27 gene. The drought-sensitive phenotype was further complemented by the introduction of the ZmIQD27-GFP fragment into the iqd27-1 mutant. The drought-sensitive phenotype of iqd27-1 line exhibited an irregular arrangement of microtubules and a reduction in the cell wall thickness of xylem vessels, resulting in impaired water transport. Overall, this discovery contributes significantly to our comprehension of the regulatory network underlying xylem development, and its manipulation could aid in the breeding of new maize varieties with beneficial traits that can withstand plant stress. Anuradha Singh

Lignification of the vascular system has been implicated as an important adaptation for drought tolerance. Using an EMS mutagenized B73 library, three alleles of a drought sensitive-like mutant were identified. The causative SNPs were mapped to the IQ67 domain (IQD)-containing protein-gene ZmIQD27. ZmIQD27 has the greatest expression in the root meristematic zone and mature xylem. The iqd27-1 homozygous mutant was more sensitive to drought as a result of reduced water movement through the vasculature. Further imaging of iqd27-1 vasculature cross sections revealed that mutant xylem cells had disorganized microtubule patterns and thinner cell walls with less lignin. In addition, iqd27-1 xylem vessels were frequently obstructed by ectopic accumulations of lignin. Similar to other IQD proteins, ZmIQD27 colocalizes with microtubules, overall suggesting that ZmIQD27 influences microtubule organization which influences xylem cell shape and lignin deposition. Finally, a transgenic IQD27-GFP line was developed that complemented many of the iqd27 mutant phenotypes. Aimee Uyehara

Li, H et al. 2023. IQ domain-containing protein ZmIQD27 modulates water transport in maize. Plant Physiol. :doi: 10.1093/plphys/kiad390.
   IQ domain-containing protein ZmIQD27 modulates water transport in maize.
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Chen, J et al. 2023. A complete telomere-to-telomere assembly of the maize genome Nature Genetics. :doi: 10.1038/s41588-023-01419-6.
   A complete telomere-to-telomere assembly of the maize genome

described the Zm00014ba assembly of Mo17

Maize is a classic model plant for complex genome studies. However, due to the large size of the maize genome and the fact that it has more than 80% repeats, there are hundreds or thousands of “gap” regions in the maize genome that have been reported so far. The Mo17 inbred line is the representative of the classic maize heterosis group Lancaster Group. Mo17 inbred lines and their derived materials have been widely used in maize production in China. Using Mo17 inbreed lines as materials, Prof. Lai’s team comprehensively utilized about 237× ONT Ultralong and about 69.4× Pacbio HiFi sequencing data to complete the latest maize genome assembly, with a size of 2,178.6 Mb. It is the first complete, gap-free sequence of the maize genome and the first complex animal or plant genome with all chromosomes fully assembled. The telomere-to-telomere of each chromosome is composed of a complete continuous sequence with base accuracy of more than 99.99%. The latest assembly not only adds 1,029 genes to the high-quality assembly of the past, but also unlocks the most structurally complex genomic gap in the maize genome that has never been assembled. The assembly of the complete Mo17 genome provides the first opportunity to explore the sequence and structural features of the most challenging regions of the maize genome assembly. The researchers found that the nucleolar tissue of maize was 26.8 Mb long and contained 2,974 45S rDNA copies, with highly complex patterns of rDNA replication and transposon insertion. Previously, species with fully assembled nucleolar tissue regions in plants contained only a few dozen copies of 45S rDNA. In addition, the researchers also found that there is an ultra-long simple sequence rich region mainly composed of TAG trinucleotide repeats in the maize genome, with a length of up to 1.56 Mb, containing nearly 300,000 TAG copies, of which the longest continuous TAG repeats are 235 kb. In addition, analysis of the complete genome assembly revealed a large number of genomic sequence and structural variations between different centromere and different subtelomere regions. These results have important implications for further understanding the complexity and function of higher plant genomes.

Chen, J et al. 2023. A complete telomere-to-telomere assembly of the maize genome Nature Genetics. :doi: 10.1038/s41588-023-01419-6.
   A complete telomere-to-telomere assembly of the maize genome
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Angela Byars-Winston et al. 2023. A randomized controlled trial of an intervention to increase cultural diversity awareness of research mentors of undergraduate students. Science. 9:eadf9705.
   A randomized controlled trial of an intervention to increase cultural diversity awareness of research mentors of undergraduate students.

Increasing cultural diversity awareness (CDA) among mentors can improve mentor interaction with mentees in terms of work interaction, psychosocial support, skills development, shaping perceptions, and improving decision-making for success in STEM. The authors in this paper describe results from a randomized controlled trial for increasing cultural diversity awareness among the mentors of undergraduate students using the established mentor training curriculum modified for increased CDA. The study involved 216 graduate students and postdoctoral mentors and 117 mentees from 32 STEM undergraduate programs in the USA participating in STEM summer programs. The study was administered using online 8-hour training and electronic surveys. The results indicated gains in CDA attitudes, mentors' CDA behaviors, and mentoring skills, among other gains. This paper illustrates the importance of training mentors to improve their CDA attitudes and behaviors for the benefit of STEM professionals. It also highlights the importance of evaluating the new DEI strategies to understand their actual benefits and use them better.

Angela Byars-Winston et al. 2023. A randomized controlled trial of an intervention to increase cultural diversity awareness of research mentors of undergraduate students. Science. 9:eadf9705.
   A randomized controlled trial of an intervention to increase cultural diversity awareness of research mentors of undergraduate students.
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Sun, GC et al. 2023. A role for heritable transcriptomic variation in maize adaptation to temperate environments. Genome Biology. 24:55.
   A role for heritable transcriptomic variation in maize adaptation to temperate environments.

In this work, Sun et al. generated 572 RNA-seq datasets from the roots of 340 maize genotypes (with 219 genotypes having >2 replicates) that were subsequently used for gene expression heritability estimation, expression GWAS (to obtain eQTLs), and GWAS for alternative splicing (to obtain sQTLs). Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression, while genes involved in anti-oxidation activity exhibited higher expression heritability. Approximately 700 genes each was associated with both a cis-eQTL and at least one cis-sQTL, and the associated eQTL and sQTL were colocalized, providing rich examples showing the joint or indenpdent regulation of the trait gene expression by the corresponding eQTL and sQTL. Fourty two independent components were captured from the 572 RNA-seq datasets, each representing the expression of 24 to 720 genes. SNPs associated with these 42 independent components were identified for GWAS and subsequently used for eQTL mapping for refined identification of lead SNPs regulating genes involved in stress response, plastic biogensis, and protein biogenesis. Transcriptional regulatory elements associated with temperate adaptation in maize were also investigated.

Sun, GC et al. 2023. A role for heritable transcriptomic variation in maize adaptation to temperate environments. Genome Biology. 24:55.
   A role for heritable transcriptomic variation in maize adaptation to temperate environments.
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Ashraf, MA et al. 2023. A polarized nuclear position specifies the correct division plane during maize stomatal development. Plant Physiol. :doi: 10.1093/plphys/kiad329.
   A polarized nuclear position specifies the correct division plane during maize stomatal development.

Asymmetric cell divisions are fundamental to plant development and produce two daughter cells with distinct cell fates. Mispositioning of the division plane can result in defects in cell identity or shape. This paper investigates the role of an outer nuclear membrane protein, MAIZE LINC KASH AtSINE-LIKE (MLKS2), in nuclear positioning and division plane orientation in maize stomatal asymmetric divisions. Interestingly, defective subsidiary cells in the mlks2 mutant are not a result of defects in cell polarization cues, but rather due to defects in nuclear polarization. Offset and unpolarized nuclei were associated with misplaced preprophase bands, a microtubule structure key to the establishment of the division site. In wild type, preprophase band formation was associated with stabilization of nuclear positioning, but mlks2 nuclei continued to move following preprophase band formation. Altogether, the mlks2 mutant provides exciting insight into the linked role of the nucleus and cytoskeleton in division plane establishment for asymmetric subsidiary mother cell divisions.

Ashraf, MA et al. 2023. A polarized nuclear position specifies the correct division plane during maize stomatal development. Plant Physiol. :doi: 10.1093/plphys/kiad329.
   A polarized nuclear position specifies the correct division plane during maize stomatal development.
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Hartwig, T et al. 2023. Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize Genome Biology. 24:108.
   Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize

In this study, Hartwig et al. performed ChIP-seq analysis to query the potential binding targets by ZmBZR1, a key component of the brassinosteroid signaling pathway. In particular, the ChIP-seq approach adopted here enabled the authors to quantify the allele-specific TF binding. In details, transgenic plants expressing ZmBES1/BZR1-YFP fusion protein was backcrossed six times with the B73 inbred line. Six independent crosses were performed between ZmBES1/BZR1-YFP/B73 and Mo17 (3x ZmBES1/BZR1-YFP/B73xMo17 and 3x Mo17xZmBES1/BZR1-YFP/B73). The resultant F1 hybrids were used for ChIP-seq analysis. Combined analysis of the ChIP-seq results identified 52,765 high-confidence BZR1 binding peaks flanking 13,208 genes in the hybrid. Allele-specific ZmBZR1 binding (ASB) has been observed for 18.3% of target genes and is enriched in promoter and enhancer regions. About a quarter of the ASB sites correlate with sequence variation in BZR1-binding motifs and another quarter correlate with haplotype-specific DNA methylation, suggesting that both genetic and epigenetic variations contribute to the high level of variation in ZmBZR1 occupancy. Comparison with GWAS data shows linkage of hundreds of ASB loci to important yield and disease-related traits.

Hartwig, T et al. 2023. Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize Genome Biology. 24:108.
   Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize
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Jarrad Hampton-Marcell et al. 2023. Leveraging national laboratories to increase Black representation in STEM: recommendations within the Department of Energy International Journal of Stem Education. 10
   Leveraging national laboratories to increase Black representation in STEM: recommendations within the Department of Energy

Dedicated programs for the recruitment, training, and engagement of minorities in STEM are limited. Furthermore, in most institutions where such programs are lacking, the support of STEM exposure and mentorship among minorities is constrained by a limited number of professors that can provide faculty mentorship and nurturing support. In this commentary, the authors describe the current and potential role of the Department of Energy (DOE) laboratories in providing a platform for mentorship and training of black students and professionals who are among the minority groups that face disproportionally more difficulty in STEM recruitment and retention. The authors describe existing and new programs involving DOE laboratories, such as collaboration with the National Association for the Advancement of Colored People (NAACP), which supports Afro Academic, Cultural, Technical, and Scientific Olympics (ACT-SO) STEM program for Black high school students, National Consortium for Graduate Degrees for Minorities in Engineering and Science (GEM) Fellowship for Black graduate students among other initiatives like the satellite STEM education centers. These programs provide platforms that enhance the acquisition of hands-on technical and soft skills relevant to STEM, such as computer programming, nanomaterial fabrication, molecular techniques, grant writing, and public speaking. The authors further provide recommendations on how DOE laboratories and other national laboratories can increasingly support high school research programs, strategic partnerships, graduate fellowships, and professional appointments to enhance recruitment, support, and retention of minorities in STEM.

Jarrad Hampton-Marcell et al. 2023. Leveraging national laboratories to increase Black representation in STEM: recommendations within the Department of Energy International Journal of Stem Education. 10
   Leveraging national laboratories to increase Black representation in STEM: recommendations within the Department of Energy
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Ting Guo et al. 2023. ZmRPN1 confers quantitative variation in pollen number and boosts hybrid seed production in maize. Plant Biotechnol J. :doi: 10.1111/pbi.14105.
   ZmRPN1 confers quantitative variation in pollen number and boosts hybrid seed production in maize.

The number of pollen grains is a critical determinant of reproductive success in seed plants and varies among species and individuals. However, in contrast with many mutant-screening studies relevant to anther and pollen development, the natural genetic basis for variations in pollen number remains largely unexplored. To address this issue, authors carried out a genome-wide association study in maize, ultimately revealing that a large presence/absence variation in the promoter region of ZmRPN1 alters its expression level and thereby contributes to pollen number variation. Molecular analyses showed that ZmRPN1 interacts with ZmMSP1, which is known as a germline cell number regulator, and facilitates ZmMSP1 localization to the plasma membrane. Importantly, ZmRPN1 dysfunction resulted in a substantial increase in pollen number, consequently boosting seed production by increasing female–male planting ratio. Together, these results uncover a key gene controlling pollen number, and therefore, modulation of ZmRPN1 expression could be efficiently used to develop elite pollinators for modern hybrid maize breeding.

Ting Guo et al. 2023. ZmRPN1 confers quantitative variation in pollen number and boosts hybrid seed production in maize. Plant Biotechnol J. :doi: 10.1111/pbi.14105.
   ZmRPN1 confers quantitative variation in pollen number and boosts hybrid seed production in maize.
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Guillotin, B et al. 2023. A pan-grass transcriptome reveals patterns of cellular divergence in crops Nature. :doi: 10.1038/s41586-023-06053-0.
   A pan-grass transcriptome reveals patterns of cellular divergence in crops

The evolutionary divergence of species is sometimes accompanied by the development of new cell types. This paper uses single cell and single nucleus transcriptomics to make comparisons across different cell types in maize (Z. mays), sorghum (S. bicolor), and Setaria (S. viridis). First, the authors identified conserved cell-type specific gene expression networks. Next, they used the ancient whole genome duplication event in maize to look at how homologous cell types diverge over time. Interestingly, gene duplicates that originated from a whole genome duplication event (homeologues) tended towards regulatory neofunctionalization or the expansion of expression to a new cell type. Regulatory neofunctionalization most often resulted from cases where one member of the pair was dominant or there was subfunctionalization (paralogs retain subfunction of ancestral gene). In addition, other evidence suggests that non- dominant homeologues are more likely to adopt new functions while the ancestral expression is preserved by the dominant homeologue. Some cell types were also found to be more likely to act as “sources” or “sinks” for new expression domains. Sinks included specialized vasculature and root cap cells, while cortex cells were more likely to act as sinks. Finally, over fifty modules of gene expression that demonstrated changed cell type expression from Setaria or sorghum to maize were identified. As an example, the divergence of the maize columella from Setaria may have been facilitated by the recruitment of the mucilage gene expression module from the cortex.

Guillotin, B et al. 2023. A pan-grass transcriptome reveals patterns of cellular divergence in crops Nature. :doi: 10.1038/s41586-023-06053-0.
   A pan-grass transcriptome reveals patterns of cellular divergence in crops
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Sun, XP et al. 2022. The role of transposon inverted repeats in balancing drought tolerance and yield-related traits in maize Nature Biotechnology. :doi: 10.1038/s41587-022-01470-4.
   The role of transposon inverted repeats in balancing drought tolerance and yield-related traits in maize

During the domestication and improvement process, maize yield has significantly increased, but this was accompanied by increased susceptibility to drought. The genomic basis underlying the selection for environmental adaptation and yield-related traits in maize remains poorly understood. To help address these questions, authors provide a large dataset covering hundreds of small RNA transcriptomes (sRNAomes) and transcriptomes under well-watered (WW) and drought-stressed (DS; a key environmental stress) conditions from a diverse population of maize accessions. Transgenic and molecular studies of Drought-Related Environment-specifc Super eQTL Hotspot on chromosome 8 (DRESH8) and ZmMYBR38, a target of DRESH8-derived small interfering RNAs, revealed a transposable element-mediated inverted repeats (TE-IR)-derived sRNA and gene-regulatory network that balances plant drought tolerance with yield-related traits. A genome-wide scan revealed that TE-IRs associate with drought response and yield-related traits that were positively selected and expanded during maize domestication. These results indicate that TE-IR-mediated posttranscriptional regulation is a key molecular mechanism underlying the trade-off between crop environmental adaptation and yield-related traits, providing potential genomic targets for the breeding of crops with greater stress tolerance but uncompromised yield.

Sun, XP et al. 2022. The role of transposon inverted repeats in balancing drought tolerance and yield-related traits in maize Nature Biotechnology. :doi: 10.1038/s41587-022-01470-4.
   The role of transposon inverted repeats in balancing drought tolerance and yield-related traits in maize
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Wang, WX et al. 2022. Integrating high-throughput phenotyping, GWAS and prediction models reveals the genetic architecture of plant height in maize. Molecular Plant. :doi: 10.1016/j.molp.2022.11.016.
   Integrating high-throughput phenotyping, GWAS and prediction models reveals the genetic architecture of plant height in maize.

Plant height (PH) is an essential trait in maize (Zea mays L.) which is tightly associated with planting density, biomass, lodging resistance and grain yield in the field. Dissecting the dynamics of maize plant architecture will be beneficial for ideotype-based maize breeding and prediction, as the genetic basis controlling PH in maize remains largely unknown. The authors developed an automated high-throughput phenotyping platform (HTP) to systematically and noninvasively quantify 77 image-based traits (i-traits) and 20 field traits (f-traits) for 228 maize inbred lines across all developmental stages. Time-resolved i-traits with novel digital phenotypes and complex correlations with agronomic traits were characterized to reveal the dynamics of maize growth. An i-trait-based genome-wide association study (GWAS) identified 4945 trait-associated SNPs, 2603 genetic loci, and 1974 corresponding candidate genes. They found that rapid growth of maize plants mainly occurs at two developmental stages, Stage 2 (S2) to S3 and S5 to S6, accounting for the final PH indicators. By integrating the plant height-association network with the transcriptome profiles of specific internodes, 13 hub genes that might play vital roles during the rapid growth were identified. The candidate genes and novel i-traits identified at multiple growth stages might be used as potential indicators for final PH in maize. The function of one candidate gene, ZmVATE, was validated to regulate plant height-related traits in maize by using genetic mutation. Furthermore, machine learning based prediction models were built for final plant height prediction based on i-traits, and predictive performance was assessed in validation across developmental stages. Moderate, strong, and very strong correlations between prediction and experimental datasets were achieved from early S4 (tenth-leaf) stage. Overall, this study provided a valuable tool for dissecting the spatiotemporal formation of specific internodes and the genetic architecture of PH, as well as resources and prediction models that are useful for molecular design breeding and predicting maize varieties with ideal plant architectures.

Wang, WX et al. 2022. Integrating high-throughput phenotyping, GWAS and prediction models reveals the genetic architecture of plant height in maize. Molecular Plant. :doi: 10.1016/j.molp.2022.11.016.
   Integrating high-throughput phenotyping, GWAS and prediction models reveals the genetic architecture of plant height in maize.
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Wang, SX et al. 2020. Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline. 13:1078-1093.
   Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline.

Non-conventional peptides (NCPs) are peptides derived from unannotated CDS in a genome. They include small open reading frame-encoded peptides that play critical role in fundamental biological process. In this study, Wang et al. performed a large-scale search of NCPs in maize and Arabiodopsis through a pipeline that integrated high-throughput mass spectra and peptidogenomics. Briefly, for maize, endogenous peptides were extracted from the leaves of B73 seedlings and analyzed by a high-resolution and high-accuracy mass spectrometer. The resultant mass spectrometry data was queried against two databases: 1) Ensembl protein database and 2) a customized peptidogenomic database that was the six-frame translations of B73 v4 genomic sequences. A total of 1993 NCPs were unambiguously assigned to a single genomic locus. These NCPs were derived from the unannotated CDS including the intergenic regions, UTRs, and introns. Transcriptomic analyses using the publicly available RNA-seq data provided transcriptional evidence for most NCPs and demonstrated that these NCPs were derived from lncRNAs and circular RNAs. Ribo-seq analysis further provided the translational evidence for 37% of the detected NCPs. A cross-reference between NCPs and quantitative genetics studies for yield traits demonstrated that NCPs were significantly enriched within trait-associated QTLs than random genomic regions. Several SNPs located within NCPs were associated with kernel length, disease, and oil and amino acid contents. Moreover, NCPs were also significantly enriched within candidate regions associated with domestication selection. Taken together, this study showed broad occurrence of translation events in unannotated genomic regions, and the resultant NCPs were likely biological functional, which has important implications for functional genomic studies.

Wang, SX et al. 2020. Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline. 13:1078-1093.
   Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline.
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Michael W Asher et al. 2023. Utility-value intervention promotes persistence and diversity in STEM. 120:e2300463120.
   Utility-value intervention promotes persistence and diversity in STEM.

Several strategies have been proposed to support attracting and retaining students in STEM fields; it is, therefore, imperative to use and test the usefulness of such strategies. This paper discusses the results from use of a utility-value intervention program in STEM for students. The authors used a randomized experiment in a large introductory chemistry class at a public university, involving 2,505 students in eight lecture sections during the fall and spring semesters. Among the students in the study, 10% comprised underrepresented and minoritized racial/ethnic groups in STEM, mainly of Hispanic, Black, and Native American origin. The intervention emphasized the personal value and usefulness to others using 500-word writing assignments, followed by an assessment 2.5 years after the intervention at the end of the junior level of study. The results indicated a positive influence of the intervention on the persistence of students in STEM degrees. This result was evidenced by an increase in the selection of additional STEM courses in semesters following the intervention and a greater likelihood of majoring in STEM at the end of the third year for students who completed the intervention. The impact was also more for students from marginalized groups. This paper describes how interventions can help in short-term and long-term retention of students in STEM fields and provide a basis for evaluating other similar strategies.

Michael W Asher et al. 2023. Utility-value intervention promotes persistence and diversity in STEM. 120:e2300463120.
   Utility-value intervention promotes persistence and diversity in STEM.
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Ren, ZB et al. 2023. Deciphering transcriptional mechanisms of maize internodal elongation by regulatory network analysis. J Exp Bot. :doi: 10.1093/jxb/erad178.
   Deciphering transcriptional mechanisms of maize internodal elongation by regulatory network analysis.

Plant height is determined by internode length and internode number in order to measure plant resistance to stalk lodging. The author deciphers the transcriptional mechanism of Internode length suppression in 10 maize cultivars via foliar application of coronatine (COR) during the V8 stage. Three cultivars have strong- (SC), five have medium- (MC), and three have weak- (WC) suppression of internode elongation. Following that, they harvested the eighth internode after 25 hours of COR treatment and performed RNA-seq to get insight into the gene expression levels of internode elongation genes. There were 7895 genes in all, with 2808, 2419, 2218, and 272 differently expressed in SC, SC-MS, MC, and WC combinations, respectively. Hormone-related genes, notably cytokinin, gibberellin, auxin, and ethylene, cell cycle regulatory factors, cell wall-related genes, and hormone responsive transcription factors, all showed much greater alterations in SC than in WC. Then, using EMSA, they confirmed the accuracy of the gene regulation network of the two major TFs (ABI7 and MYB117). Overall, their finding provides a valuable genetic resource for exploring the roles of internode elongation-related genes and determining the optimal internode length.

Ren, ZB et al. 2023. Deciphering transcriptional mechanisms of maize internodal elongation by regulatory network analysis. J Exp Bot. :doi: 10.1093/jxb/erad178.
   Deciphering transcriptional mechanisms of maize internodal elongation by regulatory network analysis.
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Li, QL et al. 2023. Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization. Planta. 257:94.
   Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization.

Maize (Zea mays) is an important crop plant with distinctive life history characteristics and structural features. In this review, the classical life cycle and life history strategies of maize are analyzed to identify spatiotemporal organogenesis properties and develop a definitive understanding of maize development. The actions of genes and hormones involved in maize organogenesis and sex determination, along with potential molecular mechanisms, are investigated, with findings suggesting central roles of auxin and cytokinins in regulating maize holistic development. Furthermore, investigation of morphological and structural characteristics of maize, particularly node ubiquity and the alternate attachment pattern of lateral organs, yields a novel regulatory model suggesting that maize organ initiation and subsequent development are derived from the stimulation and interaction of auxin and cytokinin fluxes. The comprehensive review of maize development and morphogenetic physiology will enable farmers to optimize field management and will provide a reference for de novo crop domestication and germplasm improvement using genome editing biotechnologies, promoting agricultural optimization.

Li, QL et al. 2023. Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization. Planta. 257:94.
   Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization.
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Pardo, J et al. 2023. Cross-species predictive modeling reveals conserved drought responses between maize and sorghum. 120:e2216894120.
   Cross-species predictive modeling reveals conserved drought responses between maize and sorghum.

The authors of this study aims at identifying the genes that play central and conserved role in drought response. To achieve this goal, a combined approach of k-means clustering and random forest classification was adopted to identify the drought-responsive genes. In details, RNA-seq samples were collected from the vegetative tissues of sorghum plants that were drought stressed and well-watered. The transcriptomes were first parsed into co-expressed clusters by k-means clustering and the 1st principal component of each gene cluster was used as the predictor for a random forest classifier that performed a binary classification ("drought" or "control") on the RNA-seq samples. The gene clusters with the most predictive power were considered as the core drought-responsive genes. To further increase the detection power, this predictive modeling was applied to a meta RNA-seq dataset containing 206 drought-stressed samples, 254 well-watered or recovered samples from 35 sorghum genotypes. This meta-analysis include datasets that are publicly available and the datasets generated by the same authors. Because the meta datasets were from different sources, batch effects were first removed before applying the predictive modeling. Next, the model was trained to identify the drought-responsive genes that were conserved across genotypes, developmental stages, and drought severities. The cross-validation demonstrated that the resultant model had a relatively high predictive accuracy ranged from 82 to 91%. Next, this modeling approach was used to probe the evolutionary conservation of the drought response between maize and sorghum. RNA-seq datasets were collected from 27 greenhouse-grown maize genotypes that were drought-stressed and well-watered. Based on the maize transcriptomes, the authors generated a converted expression matrix of the corresponding sorghum syntelogs to enable cross-species comparison. The previous sorghum model was retrained to only include genes having a syntenic counterpart in maize. The retrained model predicted the labels ("drought" or "control") of the converted expression datasets with 85% accuracy. This approach identified a core set of 284 genes with a conserved pattern of gene expression during drought stress in maize and sorghum. These genes are enriched in functions associated with various abiotic stress-responsive pathways as well as core cellular functions (e.g., ABA-mediated transcription factors, aquaporins, ROS scavengers, and heat shock proteins, etc.) . These findings support a broad evolutionary conservation of drought responses in C4 grasses regardless of innate stress tolerance, which could have important implications for developing climate resilient cereals.

Pardo, J et al. 2023. Cross-species predictive modeling reveals conserved drought responses between maize and sorghum. 120:e2216894120.
   Cross-species predictive modeling reveals conserved drought responses between maize and sorghum.
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Linda S. Ficht et al. 2023. Should DEI statements be included in faculty selection? Exploring legal, diversity, and validity issues International Journal of Selection and Assessment.
   Should DEI statements be included in faculty selection? Exploring legal, diversity, and validity issues

Since the adoption of DEI policies, DEI statements have been required and used in faculty positions' application, processing, and tenure procedures. Besides faculty, DEI policies and statements are widespread in public and private institutions. This paper addresses issues and dilemmas associated with DEI policies and statements in workforce selection and other settings in education and institutions directly and indirectly linked to STEM. Matters discussed include accountability for DEI policies and goals, legality, reliability, validity, and standardization of DEI statements and their requirements, and their lack of, at-workforce employment processes and misunderstanding of DEI statements on free speech rights. This paper directs us to be proactive in setting and evaluating our DEI goals and statements to better benefit from them.

Linda S. Ficht et al. 2023. Should DEI statements be included in faculty selection? Exploring legal, diversity, and validity issues International Journal of Selection and Assessment.
   Should DEI statements be included in faculty selection? Exploring legal, diversity, and validity issues
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Louai Rishmawi et al. 2023. Natural variation of maize root hydraulic architecture underlies highly diverse water uptake capacities Plant Physiol. :doi: 10.1093/plphys/kiad213.
   Natural variation of maize root hydraulic architecture underlies highly diverse water uptake capacities

Root system architecture (RSA) and its hydraulic capacity are important determinants of the spatiotemporal pattern of water intake in plants. Rishmawi et al. (2023) reported considerable variations for the surface area of primary root (SAPR), surface area of primary-lateral root (SA-LRPR), the hydraulic conductivity of the primary root (Lpr), and the number of seminal roots (SRN) among 224 inbred dent lines in maize. They then chose 13 representative lines from four clusters and investigated comprehensive root hydraulic parameters. The result showed that genotypes in the same cluster had comparable PR and SR Lpr values, which was not seen for RSA parameters. Next to investigate the genotypic variations, they took 4 lines from each of the 4 clusters and performed flow-to-pressure measurements in roots that were progressively cut from tip to base. Although the lines exhibit differences in PR length, a dramatic increase in hydraulic conductance (K) was observed which provides direct evidence for genotypic differences in xylem functional. Further, cross-sections from the tip of PR and SR revealed a positive correlation between the number and size of late meta xylem (LMX) vessels and Lpr. The authors hope to continue research with this group in the future to identify genetic controls of root hydraulic architecture.

Louai Rishmawi et al. 2023. Natural variation of maize root hydraulic architecture underlies highly diverse water uptake capacities Plant Physiol. :doi: 10.1093/plphys/kiad213.
   Natural variation of maize root hydraulic architecture underlies highly diverse water uptake capacities
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Nan, Q et al. 2023. The OPAQUE1/DISCORDIA2 myosin XI is required for phragmoplast guidance during asymmetric cell division in maize. Plant Cell. :doi: 10.1093/plcell/koad099.
   The OPAQUE1/DISCORDIA2 myosin XI is required for phragmoplast guidance during asymmetric cell division in maize.

OPAQUE1 is a myosin XI actin motor protein that localizes to the phragmoplast midline. The maize mutant opaque1 makes defective stomata through aberrant divisions of the subsidiary mother cell and guard mother cell. Subsidiary mother cells asymmetrically divide into two daughter cells of different cell fates (subsidiary cell and pavement cell) and specify cell identity through the sequential polarization of proteins to one face of the cell. However, hallmarks of cell polarity such as PAN1 localization and actin patch appear normal in the o1 mutant. Live cell imaging revealed that the o1 mutants have phragmoplast guidance defects while division site specification appears normal. Interestingly, the kinesins KIN12C, KIN12D, and KIN12E were identified as interactors through IP/MS. These kinesins are closely related to another kinesin, PHRAGMOPLAST ORIENTING KINESIN1, which has established roles in phragmoplast guidance in Arabidopsis, and point to a joint microtubule and actin mechanism for proper phragmoplast guidance.

Nan, Q et al. 2023. The OPAQUE1/DISCORDIA2 myosin XI is required for phragmoplast guidance during asymmetric cell division in maize. Plant Cell. :doi: 10.1093/plcell/koad099.
   The OPAQUE1/DISCORDIA2 myosin XI is required for phragmoplast guidance during asymmetric cell division in maize.
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Ran Fu et al. 2023. Modeling the influence of phenotypic plasticity on maize hybrid performance. Plant Commun. :100548.
   Modeling the influence of phenotypic plasticity on maize hybrid performance.

Phenotypic plasticity of crops refers to the phenomenon of individuals with the same genotypes who exhibit different phenotypes in different ecological environments, which is indicative of the ecological adaptability of crops. From the perspective of breeding, improving crop phenotypic plasticity is one of the important goals of artificial selection and an important means of breeding new crop varieties with wide adaptability and stable yield. Since the yield and quality of crops are affected by light, heat, water and other environmental factors, breeding new varieties with wide adaptability and strong stable yield is an important means to cope with global climate change. In this article, a variety of environmental parameters were analyzed and the photothermal ratio (PTR), an environmental index combining heat and light energy, was determined as the modeling variable. The researchers found that the response of maize to light, heat and photoperiod was different at different developmental stages, and the yield could be affected at an earlier stage of the vegetative stage. These results indicated that different environmental response genes regulated maize development at different periods. Using agronomic traits collected from 1428 maize inbred lines and 6210 maize hybrids in five provinces in China, the authors explored the model of phenotypic plasticity and G×E of maize. The authors modeled phenotypic plasticity in response to the environment (PPRE) in inbred and hybrid lines. PPRE can be simply described by a linear model in which the two main parameters, intercept a and slope b, reflect two classes of genes responsive to endogenous (class A) and exogenous (class B) signals that coordinate plant development. Together, class A and class B genes contribute to the phenotypic plasticity of an individual in response to the environment. The authors investigated the relationship between phenotypic plasticity and hybrid performance or yield general combining ability (GCA), and found that the parameters a and b of the two parents must be consistent in order to achieve the ideal GCA of F1 yield. Therefore, the coordinated regulation of two types of genes regulating flowering and plant height from parents in the F1 hybrid genome may be the biological basis for ensuring high and stable crop yield under different environments.

Ran Fu et al. 2023. Modeling the influence of phenotypic plasticity on maize hybrid performance. Plant Commun. :100548.
   Modeling the influence of phenotypic plasticity on maize hybrid performance.
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Sun, Q et al. 2022. A NAC-EXPANSIN module enhances maize kernel size by controlling nucellus elimination Nature communications. 13:5708.
   A NAC-EXPANSIN module enhances maize kernel size by controlling nucellus elimination

Maize early endosperm development is initiated in coordination with elimination of maternal nucellar tissues. In this study, Sun et al. identify ZmEXPB15 as a major QTL for kernel size and weight in maize, and find that it encodes an expansin protein that positively controls kernel size and weight. ZmEXPB15 is expressed specifically in the nucellus from 2 to 8 days after pollination (DAP), coincident with the nucellus elimination period, and promotes nucellus cell expansion and elimination. Then authors demonstrated that two nucellus-enriched NAC TFs, ZmNAC11 and ZmNAC29 may bind to the ZmEXPB15 promoter to activate expression and act epistatically with ZmEXPB15 in regulating kernel size by promoting nucellus programmed cell death (PCD). zmnac11;zmnac29;zmexpb15 triple mutant had more severe kernel defects compared to the single or double mutants, suggesting that the two NAC TFs regulate additional kernel related genes. Further, increased kernel weight of hybrids overexpressing ZmEXPB15 demonstrates its potential application value of maize breeding. Together, authors reveal a pathway modulating the cellular processes of maternal nucellus elimination and early endosperm development, and an approach to improve kernel weight.

Sun, Q et al. 2022. A NAC-EXPANSIN module enhances maize kernel size by controlling nucellus elimination Nature communications. 13:5708.
   A NAC-EXPANSIN module enhances maize kernel size by controlling nucellus elimination
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Tian, T et al. 2023. Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm Nature Genetics.
   Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm

Drought is a serious threat to global crop production. The identification and utilization of drought resistant germplasm resources are of great significance for genetic improvement of drought resistance. In this paper, the CIMBL55 genome was de novo assembled using PacBio Sequel technology, HiC technology, and BioNano optical map technology. The genome size of CIMBL55 is 2.15Gb, the contig N50 is 14.3 Mb, and the scaffold N50 is 223.6 Mb. The authors systematically analyzed the structural variations among 30 maize genomes including CIMBL55, as well as genotypes of the 368 maize population. They found that among the 108 drought resistance candidate genes identified in their previous work, CIMBL55 genome contains at least 65 excellent drought resistance alleles, which may be the genetic basis for excellent drought resistance of CIMBL55. Structural variation combined with differential methylation analysis revealed that some insertion sequences located near the transcription start site of the gene had significantly high CHH methylation, enriched with a large number of DTH (DNA transposon/TIR/Harbinger) like transposons. In drought sensitive materials, there are two insertion sequences upstream of ZmNAC075 and have a high methylation state, which may inhibit its expression and thereby affect drought resistance. In addition, through analysis of genomic structural variation, it was found that the 3'-UTR region of the ZmRtn16 gene in CIMBL55 lacks a sequence with a length of 28 bp, which may be beneficial to enhancing the stability of the mRNA. ZmRtn16 encodes a reticulon-like protein that interacts with subunits A and E3 of the vacuolar membrane H+- ATPase complex and facilitates its vacuolar membrane localization. In the deletion mutants of this gene, the activity of vacuolar membrane H+- ATPase decreased, and the response of stomata to drought stress weakened. Enhancing the function of ZmRtn16 in transgenic materials can significantly improve the drought resistance of maize at seedling and whole growth stages. Under field drought stress, the yield of ZmRtn16 transgenic material was significantly higher than that of the control material, without affecting its yield under normal conditions. This finding further suggests the role of vacuolar proton pumps in maize drought resistance. High quality genomic information from CIMBL55 will provide valuable information for systematic analysis of the genetic basis of maize drought resistance, and provide important targets for genetic improvement and molecular design breeding of maize drought resistance.

Tian, T et al. 2023. Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm Nature Genetics.
   Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm
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Nidia Ruedas-Gracia et al. 2022. Ten simple rules for creating a sense of belonging in your research group. 18:e1010688.
   Ten simple rules for creating a sense of belonging in your research group.

A strong sense of belonging supports positive interactions and well-being and can be instrumental in attracting and retaining people in STEM. However, such requires some set directions that leaders of research labs (groups) can use as guides. In this paper, the authors draw from their experience as grad students, postdocs, and PIs, and from the evidence-based practices on the sense of belonging that has increased the retention of systemically and historically excluded groups, to discuss ten general rules for creating a sense of belonging at the research group level. Discussed rules comprise self-reflection by group leaders, proper use of identities such as names and pronouns, proactive engagement, embodying shared lab values, transparency on lab expectations, creating opportunities for interactions and learning among members, fostering outside lab social interactions among members, and recognizing accomplishments by members, equity checks by lab leaders, regular request for feedback from members. These guides highlight steps that can support the sense of belonging for group members and are instrumental in helping success in STEM.

Nidia Ruedas-Gracia et al. 2022. Ten simple rules for creating a sense of belonging in your research group. 18:e1010688.
   Ten simple rules for creating a sense of belonging in your research group.
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Schneider, HM et al. 2023. Transcription factor bHLH121 regulates root cortical aerenchyma formation in maize. Proc Natl Acad Sci, USA. 120:e2219668120.
   Transcription factor bHLH121 regulates root cortical aerenchyma formation in maize.

Root anatomical traits have the potential to increase crop yield significantly by improving resource collection, transport, and utilization. Zm00001d006065 (ZmbHLH121) was discovered to be a major quantitative trait locus (QTL) and is highly expressed in the root cortex, implying its importance for the root cortical aerenchyma (RCA) phenotype in Zea species. The functional validation of ZmbHLH121 using transposon-tagged mutant lines (ZmbHLH121-Mu) and ZmbHLH121-CRISPR mutants significantly reduced RCA formation compared to the wild-type, whereas ZmbHLH121-OX lines showed a significant 1.4-fold increase in RCA formation, indicating that bHLH121 may play a positive role in regulating RCA formation. Furthermore, under environmental stress (such as high and low nitrogen, well-watered and water-stressed conditions), the function of ZmbHLH121-Mu significantly reduced RCA production in root node 3 under both nitrogen stress and control conditions, whereas root nodes 2 and 4 showed no significant differences, indicating that ZmbHLH121 may be involved in node-specific regulation of RCA formation.

Schneider, HM et al. 2023. Transcription factor bHLH121 regulates root cortical aerenchyma formation in maize. Proc Natl Acad Sci, USA. 120:e2219668120.
   Transcription factor bHLH121 regulates root cortical aerenchyma formation in maize.
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Dawe, RK et al. 2023. Synthetic maize centromeres transmit chromosomes across generations. Nature Plants. 9:433-441.
   Synthetic maize centromeres transmit chromosomes across generations.

A useful tool when introducing large sets of genes for improved crop resilience may be engineered small chromosomes. However, one missing piece is the ability to create synthetic centromeres, the sequences where kinetochores assemble to enable chromosome segregation. Here, the authors demonstrate that synthetic centromeres can be created in maize and transmit chromosomes to daughter cells. Synthetic centromeres were first generated by transforming plants twice– first to contain array binding sites, or repeats of a DNA sequence recognized by a DNA binding protein, and secondly with a fusion of the respective DNA binding motif (LexA) and a centromeric protein (CENH3). Targeting LexA-CENH3 proteins to the synthetic centromere recruited other centromeric proteins to form a functional centromere. Efficacy of the synthetic centromere was tested by asking whether chromosome breakage was induced by discordant segregation of the native and synthetic centromeres in mitosis and meiosis using the COLORLESS2 phenotype. Interestingly, in the absence of the histone fusion protein (Lex- CENH3), functional synthetic centromeres generated neochromosomes via chromosome breakage in about 1% of kernels from the lines containing synthetic centromeres. This demonstrated that synthetic centromeres recruited CENH3 even in the absence of the Lex- CENH3 transgene. However, neochromosomes were unstable in somatic tissues, especially embryos. This paper highlights important progress in engineering synthetic chromosomes in maize and other exciting applications of manipulating chromosome segregation.

Dawe, RK et al. 2023. Synthetic maize centromeres transmit chromosomes across generations. Nature Plants. 9:433-441.
   Synthetic maize centromeres transmit chromosomes across generations.
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Junpeng Zhan et al. 2022. Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci. Plant J. :doi: 10.1111/tpj.16045.
   Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci.

Maize anthers accumulate two classes of phase small interfering RNAs (phasiRNAs) that are 21-nucleotide and 24-nucleotide derived from intergenic long non-coding genome regions. Both 21- and 24-nucleotide phasiRNAs (21-PHAS and 24-PHAS) play crucial roles in the anther development and male fertility in grasses. To understand the transcriptional regulation of PHAS loci, a coexpression network analysis was performed using the previously published RNA-seq datasets. Ten temporal gene co-expression modules were resultantly identified, and four modules contained 21-PHAS and 24-PHAS loci. Notably, all 21-PHAS loci were assigned to coexpression module 4 that was solely expressed in the pre-meiotic stage of anther development. To identify putative transcription regulators for 21-PHAS loci and the other module 4 genes, 23 transcription factors (TFs) belonging to module 4 were transiently expressed in maize leaf protoplasts. Subsequent bulk-protoplast RNA-seq analysis demonstrated that most of the tested TFs required endogenous transcription co-regulators to fully activate the downstream gene networks in module 4. Consequently, different combinations of module 4 TFs were transiently expressed in maize leaf protoplasts and subjected to downstream single-cell (protoplast) RNA-seq. In addition, another set of TF constructs including different combinations of four TFs regulating 24-PHAS were also tested in maize leaf protoplasts. Principal component analysis of 192 protoplast transcriptomes demonstrated that distinct gene expression programs were activated by TF constructs potentially regulate 21- and 24-PHAS, respectively. However, neither combination of TF constructs reproducibly fully activate the module 4 gene networks in the individual protoplasts.

Junpeng Zhan et al. 2022. Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci. Plant J. :doi: 10.1111/tpj.16045.
   Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci.
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Cary Funk 2022. Black Americans’ views of education and professional opportunities in science, technology, engineering and math
   Black Americans’ views of education and professional opportunities in science, technology, engineering and math

As we commemorate black history month, it is pertinent to reflect on the views of Black Americans on the STEM profession and entities. In this report, PEW surveyed individuals who identified as Black Americans who had interacted with STEM entities at diverse levels. The participants included STEM professionals and young to older adults, who relayed their perspectives and experiences in their interaction with STEM entities. Important issues highlighted cover professional achievements, professional opportunism, openness and welcoming/unwelcoming nature of professional STEM groups, access to jobs, impacts of experience on professional progression in STEM, representation, and access to education and mentors, among several other issues. Some of the described situations outline issues such as encouragements and discouragements for involvement in STEM, mistreatments, positive vs. negative comments during interactions in STEM entities, matters on the sense of belonging, and the beliefs associated with STEM entities. Among the Key findings, few black adults believe that Black people have reached the highest level of success as scientists, while the opposite is reported in non-STEM fields such as athletics. Furthermore, most young black women say they have had a negative experience with routine health care in the past, would prefer to see a black health provider, and believe that they are likely to receive better treatment from black health care providers. The report is a good read for picturing the views of Black Americans on the support needed to increase their inclusion and representation in STEM at diverse levels

Cary Funk 2022. Black Americans’ views of education and professional opportunities in science, technology, engineering and math
   Black Americans’ views of education and professional opportunities in science, technology, engineering and math
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Han, LQ et al. 2022. A multi-omics integrative network map of maize Nature Genetics. :doi: 10.1038/s41588-022-01262-1.
   A multi-omics integrative network map of maize

Networks are excellent tools for the inference of regulatory relationships between functional elements in eukaroytes. However, a large-scale network map across different genetic layers is still lacking in maize. In this study, the authors integrated (1) genomic networks identified by chromatin interaction analysis (ChIA) with paired-end-tag sequencing (PET), (2) networks for all elements detectable by coexpression analyses across 31 different tissues and stages, (3) networks determined by translatomic coexpression analyses across 21 tissues and stages, and (4) protein–protein physical interactions (Zea mays PPIs (ZmPPIs), interactome) identified by the yeast two-hybrid method RLL-Y2H across the development of the maize inbred line B73. Finally, a multi- omics network map involves over 2 million interactions and more than 1400 modules, contains the genomic, transcriptomic, translatomic and proteomic layers are constructed. based on this network map, the authors investigated its potential application for the dissection of gene function in an evolutionary perspective and the exploration of gene regulating networks underlying complex traits. Furthermore, 2651 genes enriched in eight molecular subnetworks associated with flowering time (FT) are predicted, and 20 genes experimentally validated. Among them, 7 predicted FT genes were completely new genes without evidence for a function in FT in any plant species, 11 predicted FT genes were not validated genes in maize but had homologs in other species affecting FT and 2 were well-known FT maize genes associated with FT when comparing the FT of their respective mutant and WT lines either in two or more field environments or with an extremely significant difference in one environment. The 20 validated genes provided an ideal gene resource to advance understanding of the regulating network underlying maize FT. The integrative network map paves the way for the systematic prediction of novel genes controlling agronomic traits.

Han, LQ et al. 2022. A multi-omics integrative network map of maize Nature Genetics. :doi: 10.1038/s41588-022-01262-1.
   A multi-omics integrative network map of maize
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Nan, Q et al. 2022. Polarly localized WPR proteins interact with PAN receptors and the actin cytoskeleton during maize stomatal development Plant Cell. :doi: 10.1093/plcell/koac301.
   Polarly localized WPR proteins interact with PAN receptors and the actin cytoskeleton during maize stomatal development

Editorial Board Comment by Mohammad Arif Ashraf, December 2022: Maize stomata consists of a pair of guard cells and flanking subsidiary cells. These subsidiary cells are results of asymmetric cell division. Previous studies identified that BRK, PAN1, PAN2, ROPs proteins are required for the correct division plane orientation and consequently, subsidiary cell production. In this study, Nan et al. identified WPR family proteins as physical interactors of PAN receptors. Additionally, WPR family proteins (WPRA2 and WPRB2) are polarly localized in the subsidiary mother cell. In the brk1 and pan2 mutant, but not pan1, background, the polar localization of WPR is abolished. These results suggest that WPR family proteins appear after PAN2 and before PAN1. Similar to previously identified genes on this pathway, CRISPR/Cas9 knockout of Wprb1 and Wprb2 demonstrates aberrant subsidiary cells. Furthermore, authors have found that WPRB2, more specifically N-terminal 67 amino acids, interacts with F-actin. Co-expressing FABD2-YFP with WPRB2-RFP reduces the fluorescent intensity of FABD2-YFP. Altogether, this study suggests that WPR family is the new set of polarized proteins during stomatal development in maize and they regulate actin filaments at the cellular level.

Editorial Board Comment by Aimee Uyehara, February 2023: Stomata, leaf pores that enable gas exchange in plants, are generated through asymmetric divisions. Asymmetric cell divisions generate two daughter cells of different cell types. In contrast to Arabidopsis, the development of stomata in maize requires the BRICK (BRK)- PANGLOSS (PAN)-RHO FAMILY GTPASE (ROP) pathway, which acts to polarize the divisions of the subsidiary mother cell. Proteins in this pathway polarize sequentially and promote the polarized recruitment of the next protein. In this paper, authors Nan et al., 2023 identify another component of the BRK-PAN-ROP pathway called WPRs, short for WEAK CHLOROPLAST MOVEMENT UNDER BLUE LIGHT (WEB1)/PLASTID MOVEMENT IMPAIRED2 (PMI2)- RELATED proteins. Four of seventeen maize WPRs were identified through Co-IP/MS to interact with the catalytically inactive leucine-rich repeat receptor-like protein PAN2-YFP. PAN2 is required for the polarization of PAN1 in asymmetric subsidiary mother cell divisions, but there is no evidence of interaction. CFP-WPRA2 and RFP-WPRB2 polarized in subsidiary mother cells, similarly to previously characterized stomata pathway proteins. Protein-protein interaction experiments suggest that WPRA and WPRB proteins interact to form a heterodimer, but only WPRBs interact with PAN1 and PAN2. Using available fluorescent markers and BRK-PAN-ROP pathway mutants, the timing of WPR polarization was placed after PAN2 and before PAN1 polarization. The role of WPRs in subsidiary cell divisions is highlighted by CRISPR-Cas9 generated wprb1/wprb1, wprb2/wprb2 mutants that have increased subsidiary cell defects, but redundancy within the family and likely lethality of higher order mutants makes analysis challenging. Transient expression and actin pull-down assays also show that WPRB binds to actin. WPRB may destabilize actin filaments, opening up many exciting questions about the role of WPRs in the polarized divisions of the stomatal complex.

Nan, Q et al. 2022. Polarly localized WPR proteins interact with PAN receptors and the actin cytoskeleton during maize stomatal development Plant Cell. :doi: 10.1093/plcell/koac301.
   Polarly localized WPR proteins interact with PAN receptors and the actin cytoskeleton during maize stomatal development
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Kong, DX et al. 2022. UB2/UB3/TSH4-anchored transcriptional networks regulate early maize inflorescence development in response to simulated shade. Plant Cell. :doi: 10.1093/plcell/koac352.
   UB2/UB3/TSH4-anchored transcriptional networks regulate early maize inflorescence development in response to simulated shade.

In this study, Kong et al. performed a comprehensive comparative RNA-seq analysis of the shoot apices and immature tassels of maize seedlings grown under normal white light conditions or subjected to EOD-FR treatments (sampled from V3 to V9), and identified that three homologous SPL transcription factors (UB2, UB3, and TSH4) act as a central regulatory node that controls maize inflorescence development in response to shade. And the ub2 ub3 double mutant and tsh4 single mutant were almost insensitive to simulated shade treatments. Moreover, authors demonstrated that UB2/UB3/TSH4 could directly activate the expression of BIF2 and ZmTCP30 and regulate tassel branching and ear development. Taken all together, the authors analyzed the transcriptional regulation changes of tassles and ears development under maize response to shade-mimicking treatments, and identified UB2/UB3/TSH4- anchored transcriptional regulatory network of maize inflorescence development and provide valuable targets for breeding shade-tolerant maize cultivars.

Kong, DX et al. 2022. UB2/UB3/TSH4-anchored transcriptional networks regulate early maize inflorescence development in response to simulated shade. Plant Cell. :doi: 10.1093/plcell/koac352.
   UB2/UB3/TSH4-anchored transcriptional networks regulate early maize inflorescence development in response to simulated shade.
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Wang, N et al. 2023. Leaf transformation for efficient random integration and targeted genome modification in maize and sorghum Nature Plants. :doi: 10.1038/s41477-022-01338-0.
   Leaf transformation for efficient random integration and targeted genome modification in maize and sorghum

The genetic transformation and regeneration of plants with novel phenotypes was an milestone in plant biotechnology that sparked high hopes among plant scientists. The success of transformation is highly dependent on the selection of explants, which range from single cells, such as protoplasts, to embryonic tissues, such as meristem, scutellum, or cotyledons, to seedling-derived tissues, such as apical/axillary meristems, hypocotyl, or leaves, and finally to plant-based alternatives. The use of morphogenic genes Wuschel2 (Wus2) and Babyboom (Bbm) to enhance Agrobacterium-mediated transformation and/or Cas9-mediated gene editing in grass species is gaining momentum. Wang et al. (2023) describe a unique combination of promoters directing the expression of Wus2 and Bbm that stimulates direct rapid production of somatic embryos and regeneration of T0 plants through Agrobacterium-mediated transformation of seedling-derived leaf tissue infection of maize and sorghum seedling-derived early. They also show that this improved leaf transformation technique allows for genomic changes in a variety of grass species, including rice (both indica and japonica), teff, switchgrass, pearl millet, foxtail millet, and barley.

Wang, N et al. 2023. Leaf transformation for efficient random integration and targeted genome modification in maize and sorghum Nature Plants. :doi: 10.1038/s41477-022-01338-0.
   Leaf transformation for efficient random integration and targeted genome modification in maize and sorghum
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Mariel A Pfeifer et al. 2023. What I Wish My Instructor Knew: How Active Learning Influences the Classroom Experiences and Self-Advocacy of STEM Majors with ADHD and Specific Learning Disabilities. 22:ar2.
   What I Wish My Instructor Knew: How Active Learning Influences the Classroom Experiences and Self-Advocacy of STEM Majors with ADHD and Specific Learning Disabilities.

The unique potential of students suffering from attention-deficit/hyperactivity disorder (ADHD) and specific learning disorders (SLD) to contribute to STEM through their tendency for hyperfocus, higher visual processing among other skills cannot be underestimated. In this paper, the authors describe how active learning can be structured to help STEM students suffering from ADHD and SLD in their learning. The study follows a qualitative questionnaire approach with STEM college students with ADHD and SLD on how active-learning practices affected their perceived learning experiences and self-advocacy in undergraduate STEM courses. Discussed active learning practices include use of clickers, group work, course materials, the environment among others, there are also suggestions on better implementation of these practices with consideration of unique student needs and support of the self advocacy for the students. The ideas discussed in the paper are key for improving STEM education for students with ADHD and SLD.

Mariel A Pfeifer et al. 2023. What I Wish My Instructor Knew: How Active Learning Influences the Classroom Experiences and Self-Advocacy of STEM Majors with ADHD and Specific Learning Disabilities. 22:ar2.
   What I Wish My Instructor Knew: How Active Learning Influences the Classroom Experiences and Self-Advocacy of STEM Majors with ADHD and Specific Learning Disabilities.
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Yoshihara, Takeshi et al. 2022. Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism Proc Natl Acad Sci, USA. 119:e2212199119.
   Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism

Root gravitropism is an essential process for plant growth in the earth, however the regulatory mechanism for this process remains largely unknown. To uncover the genetic elements affecting root gravitropism, Yoshihara et al. (2022) adopted a quantitative trait locus mapping approach that 1) collected seedling root gravity responses from IBMRIL population in a time span of 180 min using a machine vision methodology, and 2) performed a stepwise QTL analysis to identify QTLs associated with the phenotype time series. Next, Yoshihara et al. searched one-to-one orthologs within the maize QTLs and the root gravity QTLs identified for Arabidopisis, assuming that the orthologous genes encoding conserved functions in root gravitropism may reside within both sets of QTLs. Seven one-to-one ortholog pairs were identified from 233 Arabidopsis candidate genes and 5,483 maize candidate genes. The root gravity phenotype was evaluated in the mutant lines for five maize orthologs, and four mutants exhibited varying gravitropism than the wild-type seedling. The genes correspond to the four mutants include CCT2 that participates phosphatidylcholine biosynthesis, ATG5 controlling membrane remodeling during autophagy, UGP2 that is involved in cellulose and callose biosynthesis, and FAMA that is a bHLH transcription factor. In summary, this paper identified novel genes contributing to root gravitropism by precise phenotyping of root gravity response in mapping populations of Arabidopsis and maize, and by one-to-one orthology analysis between the QTLs of these two distantly related species.

Yoshihara, Takeshi et al. 2022. Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism Proc Natl Acad Sci, USA. 119:e2212199119.
   Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism
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Guan, JC et al. 2022. Maize domestication phenotypes reveal strigolactone networks coordinating grain size evolution with kernel-bearing cupule architecture. Plant Cell. :doi: 10.1093/plcell/koac370.
   Maize domestication phenotypes reveal strigolactone networks coordinating grain size evolution with kernel-bearing cupule architecture.

Maize is the most staple food of the word, was domesticated from its wild grass ancestor, teosinte. Domestication event was not only for seed size and number, but also for seed architecture features (casing to cob transition), which resulted in ten-fold increase in grain mass. So far, only one locus, Tga1 has been identified, contributing to partial transition of ear architecture in modern maize. In this paper, Guan et al. (2022) demonstrates that strigolactones (SLs) regulate many aspects of maize phenotypes. They observed the pleotropic phenotype including smaller ear and kernel-size shared with SL-deficient mutants (ccd8). They used three approaches, ccd8-specific revertant, application of synthetic SL analog, and disruption of SL receptor D14a, D14b, to support a role of SL signaling in maize ear architecture and seed development. Because SL-deficient mutants (ccd8) and TGa1 shared distinct phenotypic features, they developed a ccd8/tga1 double recessive line to test the overlap at the genetic level; however, complementary effects of the ccd8 and tga1 genes were evident with intermediate effects on phenotypes. Furthermore, RNA sequencing data suggest that TGA1 and SL signaling share common direct and/or independent pathways in ear development. Potential interactions between the SL signaling network (D14a, D53) and TGA1 support SL signaling contributions to ear architecture via effects on TGA1 protein. Overall, this study reveals that the SL network's roles include increasing maize seed size and, more importantly, coordinating increased kernel growth with remodeling of protective maternal tissues.

Guan, JC et al. 2022. Maize domestication phenotypes reveal strigolactone networks coordinating grain size evolution with kernel-bearing cupule architecture. Plant Cell. :doi: 10.1093/plcell/koac370.
   Maize domestication phenotypes reveal strigolactone networks coordinating grain size evolution with kernel-bearing cupule architecture.
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Zhang, M et al. 2022. Positional cloning and characterization reveal the role of a miRNA precursor gene ZmLRT in the regulation of lateral root number and drought tolerance in maize J Integr Plant Biol. :doi: 10.1111/jipb.13408..
   Positional cloning and characterization reveal the role of a miRNA precursor gene ZmLRT in the regulation of lateral root number and drought tolerance in maize

miR166a is actually in chromosome 6; in B73 v5, sequence provided aligns best to miR166e, which is included in pza03317 (in 5L). This is likely the candidate gene described as it is near the other two "neighboring" genes described (hb41 and orc2). In v3 & v4; sequence provided aligns best to miR166d (in 5S); this is not likely the correct candidate.

The number of lateral roots is a crucial determinant of maize drought tolerance. To explore the genes controlling this trait, the authors constructed recombinant inbred lines using Zong3 (with many lateral roots) and 87-1 (with few lateral roots). A candidate gene (ZmLRT) within a major QTL (qLRT5-1) was identified by Map-based cloning. ZmLRT encodes the microRNA miR166a and is highly expressed in root tips and lateral root primordia. Knocking-out ZmLRT increased the number of lateral roots, while overexpression of ZmLRT decreased the number of lateral roots, confirming that ZmLRT is the causal gene underlying qLRT5-1. The expression level of ZmLRT is lower in Zong3, compared with 87-1, leading to higher expression levels of the target genes of ZmLRT (five development-related class-III homeodomain-leucine zipper genes), and in turn, more lateral roots in Zong3. Knocking-out of ZmLRT enhanced drought tolerance of maize seedlings. This study highlights ZmLRT as a new target for improving drought tolerance in maize.

Zhang, M et al. 2022. Positional cloning and characterization reveal the role of a miRNA precursor gene ZmLRT in the regulation of lateral root number and drought tolerance in maize J Integr Plant Biol. :doi: 10.1111/jipb.13408..
   Positional cloning and characterization reveal the role of a miRNA precursor gene ZmLRT in the regulation of lateral root number and drought tolerance in maize
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Yin, LW et al. 2022. The heterogeneity in the landscape of gene dominance in maize is accompanied by unique chromatin environments Mol Biol Evol. :doi: 10.1093/molbev/msac198.
   The heterogeneity in the landscape of gene dominance in maize is accompanied by unique chromatin environments

Whole-genome duplication (WGD) has been an important contributor to genetic novelty throughout the evolutionary history of eukaryotes. Subgenome dominance after whole-genome duplication (WGD) has been observed in many plant species. However, the degree to which the chromatin environment affects this bias has not been explored. In this study, Yin et al. compared the dominant subgenome (maize1) and the recessive subgenome (maize2) concerning patterns of sequence substitutions, genes expression, transposable element accumulation, small interfering RNAs, DNA methylation, histone modifications, and accessible chromatin regions (ACRs). They separated the maize genome into pericentromeric regions and chromosomal arms and performed comprehensive genomic and epigenomic comparisons between maize1 and maize2. They found that the location of maize1 genes in chromosomal arms is pivotal for maize1 to maintain its dominance regardless of where their maize2 homoeologs are located. Moreover, no significant bias was detected in the majority of the measured variables between maize1 and maize2 homoeologous genes when both of them are located in pericentromeric regions, suggesting that the selective forces that shape dominance are absent in these regions. Most importantly, they observed that bias in these parameters in ACRs is less pronounced in the recombination-suppressed pericentromeric regions. In summary, their research demonstrates that the chromatin environment is an important factor that may shape the bias of subgenomes in maize.

Yin, LW et al. 2022. The heterogeneity in the landscape of gene dominance in maize is accompanied by unique chromatin environments Mol Biol Evol. :doi: 10.1093/molbev/msac198.
   The heterogeneity in the landscape of gene dominance in maize is accompanied by unique chromatin environments
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Nan, Q et al. 2022. Polarly localized WPR proteins interact with PAN receptors and the actin cytoskeleton during maize stomatal development Plant Cell. :doi: 10.1093/plcell/koac301.
   Polarly localized WPR proteins interact with PAN receptors and the actin cytoskeleton during maize stomatal development

Editorial Board Comment by Mohammad Arif Ashraf, December 2022: Maize stomata consists of a pair of guard cells and flanking subsidiary cells. These subsidiary cells are results of asymmetric cell division. Previous studies identified that BRK, PAN1, PAN2, ROPs proteins are required for the correct division plane orientation and consequently, subsidiary cell production. In this study, Nan et al. identified WPR family proteins as physical interactors of PAN receptors. Additionally, WPR family proteins (WPRA2 and WPRB2) are polarly localized in the subsidiary mother cell. In the brk1 and pan2 mutant, but not pan1, background, the polar localization of WPR is abolished. These results suggest that WPR family proteins appear after PAN2 and before PAN1. Similar to previously identified genes on this pathway, CRISPR/Cas9 knockout of Wprb1 and Wprb2 demonstrates aberrant subsidiary cells. Furthermore, authors have found that WPRB2, more specifically N-terminal 67 amino acids, interacts with F-actin. Co-expressing FABD2-YFP with WPRB2-RFP reduces the fluorescent intensity of FABD2-YFP. Altogether, this study suggests that WPR family is the new set of polarized proteins during stomatal development in maize and they regulate actin filaments at the cellular level.

Editorial Board Comment by Aimee Uyehara, February 2023: Stomata, leaf pores that enable gas exchange in plants, are generated through asymmetric divisions. Asymmetric cell divisions generate two daughter cells of different cell types. In contrast to Arabidopsis, the development of stomata in maize requires the BRICK (BRK)- PANGLOSS (PAN)-RHO FAMILY GTPASE (ROP) pathway, which acts to polarize the divisions of the subsidiary mother cell. Proteins in this pathway polarize sequentially and promote the polarized recruitment of the next protein. In this paper, authors Nan et al., 2023 identify another component of the BRK-PAN-ROP pathway called WPRs, short for WEAK CHLOROPLAST MOVEMENT UNDER BLUE LIGHT (WEB1)/PLASTID MOVEMENT IMPAIRED2 (PMI2)- RELATED proteins. Four of seventeen maize WPRs were identified through Co-IP/MS to interact with the catalytically inactive leucine-rich repeat receptor-like protein PAN2-YFP. PAN2 is required for the polarization of PAN1 in asymmetric subsidiary mother cell divisions, but there is no evidence of interaction. CFP-WPRA2 and RFP-WPRB2 polarized in subsidiary mother cells, similarly to previously characterized stomata pathway proteins. Protein-protein interaction experiments suggest that WPRA and WPRB proteins interact to form a heterodimer, but only WPRBs interact with PAN1 and PAN2. Using available fluorescent markers and BRK-PAN-ROP pathway mutants, the timing of WPR polarization was placed after PAN2 and before PAN1 polarization. The role of WPRs in subsidiary cell divisions is highlighted by CRISPR-Cas9 generated wprb1/wprb1, wprb2/wprb2 mutants that have increased subsidiary cell defects, but redundancy within the family and likely lethality of higher order mutants makes analysis challenging. Transient expression and actin pull-down assays also show that WPRB binds to actin. WPRB may destabilize actin filaments, opening up many exciting questions about the role of WPRs in the polarized divisions of the stomatal complex.

Nan, Q et al. 2022. Polarly localized WPR proteins interact with PAN receptors and the actin cytoskeleton during maize stomatal development Plant Cell. :doi: 10.1093/plcell/koac301.
   Polarly localized WPR proteins interact with PAN receptors and the actin cytoskeleton during maize stomatal development
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A M Aramati Casper et al. 2022. "It's completely erasure": A Qualitative Exploration of Experiences of Transgender, Nonbinary, Gender Nonconforming, and Questioning Students in Biology Courses. CBE life sciences education. 21:ar69.
   "It's completely erasure": A Qualitative Exploration of Experiences of Transgender, Nonbinary, Gender Nonconforming, and Questioning Students in Biology Courses.

Gender identity issues are emerging, making more urgent the need to make STEM fields more inclusive to queer individuals. In this paper, the authors used a queer-inclusive gender item approach to select participants for inclusion in a qualitative study where they used interviews to obtain views on student-based encounters on aspects of undergraduate biology courses that are exclusionary on the basis of sex, gender, sexual attraction, and orientation that harm their sense of belonging, career choice, perceptions, and participation, among other impacts. They identified the existence of master narratives in biology courses that cause a range of harms, the implicit exclusive nature that arises, how students use resilience strategies to cope and the potential of biology to be queer-inclusive which they describe as key themes. This paper is interesting because it describes and makes apparent the exclusionary nature of existing undergraduate biology courses and their associated impacts on LGBTQ and transgender students.

A M Aramati Casper et al. 2022. "It's completely erasure": A Qualitative Exploration of Experiences of Transgender, Nonbinary, Gender Nonconforming, and Questioning Students in Biology Courses. CBE life sciences education. 21:ar69.
   "It's completely erasure": A Qualitative Exploration of Experiences of Transgender, Nonbinary, Gender Nonconforming, and Questioning Students in Biology Courses.
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Klein, SP et al. 2022. The evolution and function of transposons in epigenetic regulation in response to the environment. Curr Opin Plant Biol. 69:102277.
   The evolution and function of transposons in epigenetic regulation in response to the environment.

In this review the authors discuss the many roles in regulation that transposable elements(TEs) have been shown to have in various plant species. Far from being the “junk DNA” that they have been called previously, transposable elements should be considered and accounted for when investigating regulation. Many transposon families have been shown to alter regulatory regions of genes by either disrupting them or introducing new transcription factor binding sites, therefore they could be useful in developing more stress resilient crops. However, when considering transposons as a genetic tool for creating stress resilience, we must be aware of the differences between crop species transposon ecosystems and that we can’t reliably use a transposon from one species in another to induce a response. This is a great summary of the burgeoning field of transposon stress response.

Klein, SP et al. 2022. The evolution and function of transposons in epigenetic regulation in response to the environment. Curr Opin Plant Biol. 69:102277.
   The evolution and function of transposons in epigenetic regulation in response to the environment.
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Huang, YC et al. 2022. THP9 enhances seed protein content and nitrogen-use efficiency in maize Nature. :doi: 10.1038/s41586-022-05441-2.
   THP9 enhances seed protein content and nitrogen-use efficiency in maize

The domestication of teosinte, the wild ancestor of maize, into modern maize focused mostly on yield and starch content, while protein content and flavor received less consideration. Variation in seed protein content (α-zein) and asparagine level reveals that the loci that control seed protein content are genetically variable between teosinte, Zea mays subsp. parviglumis (Ames accession 21814) and modern maize inbreds (B73). In this paper, the researchers have created a high-quality teosinte haplotype assembly for comparing α-zein loci in Ames 21814 and other inbreds and decode the haplotype information of a single F1 plant using a trio-binning approach. On chromosome 9, they identified TEOSINTE HIGH PROTEIN 9 (THP9) as a key quantitative trait locus for high-protein content (α-zein). Fine mapping of THP9 revealed three genes (Zm00001d047732, Zm00001d047736 and Zm00001d047737). Zm00001d047736, which corresponds to Teo09G002926, encodes an asparagine synthetase 4 (ASN4) enzyme that is abundantly expressed in teosinte with an intact ASN4 gene but not in the B73 inbred, in which a loss in the tenth intron of THP9-B73 results in improper splicing of THP9-B73 transcripts. Transgenic expression of THP9-teosinte in B73 resulted in a significant increase in seed protein content. Introgression of THP9-teosinte into current maize inbreds and hybrids substantially boosted the accumulation of free amino acids, particularly asparagine, throughout the plant and increased the seed protein content without affecting yield. THP9-teosinte appears to boost nitrogen-use efficiency, which is crucial for fostering high yields in low-nitrogen environments. (Anuradha Singh, November 2022)

As early as 9,000 years ago, the ancestors of humans in the Americas began to domesticate maize, gradually transforming a wild maize called "teosinte" into an edible crop. During the domestication process, the starch content and yield of maize continuously increased, making it one of the most widely used feed today. However, at the same time, this domestication process also sacrificed some of the excellent qualities of maize. Surprisingly, the protein content of the ancestral maize seeds far exceeds that of modern maize. However, the mechanism behind the high protein content in wild maize seeds has been a long-standing unresolved century-old problem, and the key genes that control the total protein content of maize and efficient nitrogen utilization have not been found. The research team first successfully assembled a heterozygous and complex wild maize haploid genome through the combination of third-generation sequencing technology and three-dimensional genomics, which was used for the positioning and cloning of high protein genes in wild maize. Through map-based cloning, a major quantitative trait locus for high protein content, TEOSINTE HIGH PROTEIN 9 (THP9), was identified on chromosome 9. This gene encodes asparagine synthetase 4 (ASN4), and ASN is the center of nitrogen metabolism, responsible for the synthesis of asparagine. Asparagine plays a central role in nitrogen cycling and acts as a nitrogen donor in intermolecular transfer reactions of amino groups. Therefore, the level of asparagine in plants is closely related to seed protein content. The study found that the excellent gene THP9-T in wild maize was significantly upregulated, while the mutated form THP9-B, in B73 and some maize inbred lines, resulted in lower expression of ASN4. After introducing the THP9-T gene into modern maize inbred lines and hybrids, the accumulation of free amino acids, especially asparagine, in maize plants was greatly increased, and the seed protein content was also increased without affecting the yield. THP9-T can improve nitrogen utilization efficiency and is of great significance for promoting high yield under low nitrogen conditions. (Jun Yan, September 2023)

Huang, YC et al. 2022. THP9 enhances seed protein content and nitrogen-use efficiency in maize Nature. :doi: 10.1038/s41586-022-05441-2.
   THP9 enhances seed protein content and nitrogen-use efficiency in maize
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Virginia Gewin 2021. How to include Indigenous researchers and their knowledge. 589:315-317.
   How to include Indigenous researchers and their knowledge.

While some structures have been established to increase the representation of Indigenous researchers in academia, participation within STEM fields remains extremely low. In this article, Native American and Indigenous scientists discuss ways to support and uplift Indigenous scholars. The researchers suggest integrating Western and Indigenous knowledge, conducting research that benefits Indigenous communities, and centering Indigenous scholars and their perspectives as researchers. Data sovereignty is paramount in many Indigenous communities, particularly after examples of past data misuse by academic research institutions. Collaborations with Indigenous communities can take time, so research with these communities should be conducted at a time when researchers do not feel pressured to publish quickly. White scholars can be better allies through active collaborations, rather than Tokenism, actively seeking Native American perspectives in seminars, and identifying concrete actions they can take as Allies for their Native American and Indigenous colleagues. As we celebrate Indigenous People’s Day, it is pivotal to reflect on how to support their representation and inclusion in STEM fields. Lindsay Penelope

Virginia Gewin 2021. How to include Indigenous researchers and their knowledge. 589:315-317.
   How to include Indigenous researchers and their knowledge.
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Le, L et al. 2022. A spatiotemporal transcriptomic network dynamically modulates stalk development in maize Plant Biotechnol J. :doi: 10.1111/pbi.13909.
   A spatiotemporal transcriptomic network dynamically modulates stalk development in maize

Other genes expressed during stalk development: Zm00001d027938 Zm00001d015845 Zm00001d025564 Zm00001d033710 Zm00001d013720 Zm00001d050079 Zm00001d019552

The growth and development of the maize stalk are essential in determining the final plant height. In conjunction with cell division, cell wall synthesis, and the formation of vascular bundles, the stalk of a developing maize plant expands in a sigmoidal pattern. To better comprehend the gene regulatory network of maize stalk development, stalks at the elongation (ES-V14) and maturation (MS-R6) stages were transcriptionally investigated. According to their expression patterns, 13,964 genes were clustered into four unique zones and nine coexpression modules. In addition, the authors found differentially expressed genes related with internode maintenance, elongation, and division, as well as the roles of hormones and transcription factors in the transition of stalk development. Further, coexpression network analysis identifies phenotype-specific network modules and hormone-related hub genes (2 cytochrome P450 family genes (ZmD1), 4 auxin-related genes, and 1 histone acetyltransferase). Finally, CRISPR/Cas9-mediated molecular analysis verified that the lack of ZmD1 function resulted in a shorter stature and a thicker culm than the wild type, establishing the essential role of the ZmD1 gene in maize stalk development. Overall, this study uncovered a previously unknown global transcriptome and coexpression network regulating stalk development in maize, with a notable feature of dynamic changes in transcript profiles from the ES to the MS. Anuradha Singh, 2022

Le, L et al. 2022. A spatiotemporal transcriptomic network dynamically modulates stalk development in maize Plant Biotechnol J. :doi: 10.1111/pbi.13909.
   A spatiotemporal transcriptomic network dynamically modulates stalk development in maize
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Dai, DW et al. 2022. Paternal imprinting of dosage-effect defective1 contributes to seed weight xenia in maize Nature communications. 13:5366.
   Paternal imprinting of dosage-effect defective1 contributes to seed weight xenia in maize

In this study the authors use a mutant of the dosage-effect defective 1 (ded1) gene to study the impacts of the mutation on seed weight and size in reciprocal crosses. The authors were also able to map the gene to the locus Zm00001d033265 in the reference assembly of B73 version 4, as the version 5 assembly annotation included an alternatively spliced transcript which was not supported by their sequencing. Through this ded1 is confirmed to be a transcription factor. In reciprocal crosses of ded1-ref and ded1 in 3 lineage backgrounds the authors found that when paternally inherited the ded1-ref was capable of supporting endosperm and embryo development to nearly normal size, however when inherited maternally (with the paternal allele being non-functional) they found a significant decrease in seed size and weight. Additionally through a differential expression analysis with mutant and WT siblings they found over 2000 genes that are differentially expressed with many involved in the acquisition of nutrients to the endosperm or predicted functions in the endosperm-embryo interface of the developing kernel. Kaitlin Higgins, 2022

Dai, DW et al. 2022. Paternal imprinting of dosage-effect defective1 contributes to seed weight xenia in maize Nature communications. 13:5366.
   Paternal imprinting of dosage-effect defective1 contributes to seed weight xenia in maize
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Zhang, M et al. 2022. A teosinte-derived allele of an HKT1 family sodium transporter improves salt tolerance in maize Plant Biotechnol J.
   A teosinte-derived allele of an HKT1 family sodium transporter improves salt tolerance in maize

It has long been established that salt tolerance of crops can be improved by increased shoot Na+ exclusion. However, key players in Na+ exclusion have not been extensively identified. In this study, by association analysis using a panel of 513 inbred lines of maize, the authors identified ZmNC3 (Zea mays L. Na+ Content 3) as an important locus controlling maize shoot Na+ content. An HKT1 family gene, ZmHKT1;2, was identified as the causal gene for this locus. ZmHKT1;2 encodes a Na+-preferential transporter localized in the plasma membrane, and mediates shoot Na+ exclusion. A nonsynonymous SNP (SNP947-G) increases the Na+ transport activity of ZmHKT1;2, promoting shoot Na+ exclusion and salt tolerance in maize. Interestingly, although the SNP947-G allele is present at a high frequency (43%) in teosinte, its frequency in maize is quite low (6.1%). Introgression of the SNP947-G allele into elite maize germplasms reduces shoot Na+ content and promotes salt tolerance, indicating its potential in developing salt-tolerant maize varieties. Hai Wang, 2022

Zhang, M et al. 2022. A teosinte-derived allele of an HKT1 family sodium transporter improves salt tolerance in maize Plant Biotechnol J.
   A teosinte-derived allele of an HKT1 family sodium transporter improves salt tolerance in maize
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Rocío Joo et al. 2022. Ten simple rules to host an inclusive conference. 18:e1010164.
   Ten simple rules to host an inclusive conference.

In this paper, the authors outline some general rules for organizing inclusive conferences, conceptualized by the committee of the 2021 useR! statistical computing conference and then improved from what was learned in the planning, implementation, and debrief of the conference. They cover actionable rules on achieving diversity by starting with a clear diversity vision, creating a safe environment, designing the organizing team, countering bias, virtual aspects, accessibility, language, communication, finance, and post-conference evaluation. Practical examples accompany these rules; for example, in an in-person meeting, they suggest considering a safe environment that may include dedicated childcare and religious spaces. They acknowledge diversity of inclusion needs and impacts of many competing issues, including financing and suggest clarity of vision and logical planning. Organizing inclusive scientific conferences is vital for scientific prosperity; therefore outlines or general frameworks that can be adopted to achieve inclusive conferences are essential. Andrew Egesa, 2022

Rocío Joo et al. 2022. Ten simple rules to host an inclusive conference. 18:e1010164.
   Ten simple rules to host an inclusive conference.
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Yang, B et al. 2022. The sugar transporter ZmSUGCAR1 of the Nitrate Transporter 1/Peptide Transporter family is critical for maize grain filling Plant Cell. :doi: 10.1093/plcell/koac256.
   The sugar transporter ZmSUGCAR1 of the Nitrate Transporter 1/Peptide Transporter family is critical for maize grain filling

Grain development depends on the efficient transport of nutrients from maternal to filial seed tissues. Among many nutrients, soluble sugars are essential to grain filling and yield. So far, many transporters belonging to the sugars will eventually be exported transporters (SWEETs) family have been identified. However, how sugars are imported into developing grains of major crops, remains poorly understood. In this paper, Yang et al. screened an ethyl methanesulfonate (EMS)-mutagenized library for homozygous mutants with altered kernel size, to investigate the mechanism regulating seed development of maize. By performing map-based cloning, they discovered that the causal gene for the defective kernel phenotype was an NRT1/PTR-type transporter, which typically transports nitrate, peptides, and ions. However, the researchers demonstrated that this NRT1/PTR-type transporter was a sugar transporter and named ZmSUGCAR1, by performing tracer-labeled sugar uptake and serial electrophysiological studies including two-electrode voltage-clamp, non-invasive microelectrode ion flux estimation assays in Xenopus laevis oocytes and patch clamping in HEK293T cells. Furthermore, by doing RT-qPCR and subcellular localization analysis, they found that ZmSUGCAR1 is specifically expressed in the basal endosperm transfer layer and loss-of-function mutation of ZmSUGCAR1 caused significantly decreased sucrose and glucose contents. Finally, they illustrated that the orthologs of ZmSUGCAR1 from wheat and sorghum displayed similar sugar transport activities, thus supporting the functional conservation of this transporter in closely related cereal species. In summary, the discovery of ZmSUGCAR1 uncovers a type of sugar transporter essential for grain development and opens potential avenues for genetic improvement of seed-filling and yield in maize and other grain crops. Beibei Lui, 2022

Yang, B et al. 2022. The sugar transporter ZmSUGCAR1 of the Nitrate Transporter 1/Peptide Transporter family is critical for maize grain filling Plant Cell. :doi: 10.1093/plcell/koac256.
   The sugar transporter ZmSUGCAR1 of the Nitrate Transporter 1/Peptide Transporter family is critical for maize grain filling
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Qiang, ZQ et al. 2022. The transcription factor ZmMYB69 represses lignin biosynthesis by activating ZmMYB31/42 expression in maize Plant Physiol. 189:1916-1919.
   The transcription factor ZmMYB69 represses lignin biosynthesis by activating ZmMYB31/42 expression in maize

Lignin provides mechanical support to plants, but its presence reduces the enzymatic digestion and consequently makes it economically less attractive for biotechnology industry. Two well studied transcription factors, ZmMYB31 and ZmMYB42 repress lignin biosynthetic genes in maize. But the upstream regulation of the lignin biosynthesis is unknown. In this study, Qiang et al. discovered an upstream regulator, ZmMYB69, of this pathway. Overexpression of ZmMYB69 increases cell wall thickness and lignin content; and the CRISPR-Cas9 knockout lines demonstrated opposite effects. They also found that overexpression of ZmMYB69 induces the expression of ZmMYB31 and ZmMYB42; but reduces the expression of known lignin biosynthetic genes (ZmCCR3, Zm4CL3, and ZmCOMT1). This data indicates that ZmMYB69 positively regulates the expression of ZmMYB31 and ZmMYB42. Further experiments confirmed that both lignin biosynthetic pathway repressors, ZmMYB31 and ZmMYB42, are under the direct transcriptional regulation of ZmMYB69. This work highlighted the mechanism of ZmMYB69-mediated lignin biosynthesis inhibition to facilitate the extraction of more sugar from maize. Arif Ashraf, 2022

Qiang, ZQ et al. 2022. The transcription factor ZmMYB69 represses lignin biosynthesis by activating ZmMYB31/42 expression in maize Plant Physiol. 189:1916-1919.
   The transcription factor ZmMYB69 represses lignin biosynthesis by activating ZmMYB31/42 expression in maize
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Christian Damian Lorenzo et al. 2022. BREEDIT: a multiplex genome editing strategy to improve complex quantitative traits in maize Plant Cell. :doi: 10.1093/plcell/koac243.
   BREEDIT: a multiplex genome editing strategy to improve complex quantitative traits in maize

Agronomic traits are often under the influence of multiple genes and/or many small effect quantitative trait loci (QTLs), making the study of these traits slow when attempting to stack mutant alleles. Multiplexing guide RNAs for CRISPR/Cas9 editing is established in multiple systems and is taken advantage by Lorenzo et al. In their BREEDIT pipeline, multiplex vectors are transformed into Cas9 homozygotes. This generates an assortment of edits dependent on both the T0 plant and multiplexed vector. These T0 are then selected for crossing schema that maximize editing coverage either within an editing vector or in combination with other editing vectors. Finally, the T1 can be selfed to generated assorted genotypes in the T2 and beyond. Applying their pipeline to suits of related genes, Lorenzo et al. demonstrate that ability to phenotype at the population level these edited plant and determine which genes or combination of genes might be the biggest contributor to a given mutant phenotype. In addition to the proof-of-concept for highly multiplexed and stacked editing across generations, Lorenzo et al. characterize the types of editing taking place across generations. Most (73%) of the target loci were edited to either heterozygous or homozygous loss of function mutant in the T0. Continually de novo edits in the T1 and T2 resulted in all but one target gene being edited by the T2. This work provides a framework for targeting complex, polygenic traits and further describes of the transgenerational editing behavior of Cas9 in maize. Lander Geadelmann, 2022

Christian Damian Lorenzo et al. 2022. BREEDIT: a multiplex genome editing strategy to improve complex quantitative traits in maize Plant Cell. :doi: 10.1093/plcell/koac243.
   BREEDIT: a multiplex genome editing strategy to improve complex quantitative traits in maize
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Diego Kozlowski et al. 2022. Intersectional inequalities in science. Proceedings of the National Academy of Sciences of the United States of America. 119
   Intersectional inequalities in science.

Supporting more representation of minority populations in STEM areas is a key strategy to promoting diversity, equity, and inclusion in STEM, which eventually improves the performance of STEM disciplines themselves. However, limited appreciation of the impacts of the existing inequalities in STEM can slow progress. The authors of this paper investigate the impacts of existing intersectional inequalities in the US Scientific workforce and its associated impacts on knowledge creation. They used the first authors of over five million publications between 2008 and 2019. The authors observed links in the identity of scientists, their research topics, funding, publication, and impacts of their work in terms of citations. These observations indicated that areas in which minority populations were underrepresented in their publication record or funding level, required focused support in funding to attract representation. This paper is interesting because it illustrates the impacts of intersectional inequities in the scientific workforce and proposes better approaches in promoting diversity, equity, and inclusion. Andrew Egesa, 2022

Diego Kozlowski et al. 2022. Intersectional inequalities in science. Proceedings of the National Academy of Sciences of the United States of America. 119
   Intersectional inequalities in science.
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Hao Wu et al. 2022. Rearrangement with the nkd2 promoter contributed to allelic diversity of the r1 gene in maize (Zea mays) Plant J.
   Rearrangement with the nkd2 promoter contributed to allelic diversity of the r1 gene in maize (Zea mays)

The gene R1 is well known for its allelic diversity and contribution to the understanding of Ac/Ds transposable elements. In this paper, the authors take our understanding of the diversity of this locus one step further by investigating the promoter regions of these alleles. Ultimately they find that a portion of the gene nkd2 upstream of its third exon shares sequence homology with the promoter region of R1-st, and that a rearrangement of the homologous regions is in part responsible for the diversity we see. Additionally, they found elevated levels of R1-sc in endosperm despite not seeing accumulation of anthocyanin. The authors discuss several possibilities for this surprising find as well as the evidence of R1 controlling downstream processes in maize endosperm development. Kaitlin Higgins, 2022

Hao Wu et al. 2022. Rearrangement with the nkd2 promoter contributed to allelic diversity of the r1 gene in maize (Zea mays) Plant J.
   Rearrangement with the nkd2 promoter contributed to allelic diversity of the r1 gene in maize (Zea mays)
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Gui, ST et al. 2022. A pan-Zea genome map for enhancing maize improvement Genome Biology. 23:178.
   A pan-Zea genome map for enhancing maize improvement

Genetic diversity in the maize genome has been extensively studied, with a number of genomes de novo assembled, and thousands of inbred lines resequenced. However, there are still several lineages within the Zea genus whose genomic composition is still unclear. In this study, Gui et. al. constructed de novo draft assemblies of 721 accessions, including 507 diverse maize inbred lines, 31 landrace individuals, and 183 teosinte individuals. The authors then constructed an approximately 6.71-Gb pan-Zea genome from 11 public genome assemblies and the draft assemblies of 721 accessions. Around 4.57 Gb non-B73 reference sequences were found from fragmented de novo assemblies. The authors annotated a total of 59 thousand pan-Zea genes and found that around 44% of them were dispensable. In total ~0.26 million common SVs were identifed and genotyped in a maize association mapping panel. Potential roles of PAV during domestication of maize were investigated. Combining genetic analyses with multi-omics data, the authors showed associations between SVs and complex agronomic traits. Taken together, the pan-Zea genome represents an important resource for understanding maize domestication and future improvement. Hai Wang, 2022

Gui, ST et al. 2022. A pan-Zea genome map for enhancing maize improvement Genome Biology. 23:178.
   A pan-Zea genome map for enhancing maize improvement
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Wang, G et al. 2022. An MCIA-like complex is required for mitochondrial complex I assembly and seed development in maize Molecular Plant.
   An MCIA-like complex is required for mitochondrial complex I assembly and seed development in maize

A mitochondria is a double membrane bound organelle that synthesizes cellular ATP by oxidative phosphorylation (OXPHOS). The OXPHOS machinery consists of complexes I, II, III, and IV, as well as F1FO-ATP synthase (complex V). Plant respiratory complex I is made up of 49 subunits, of which 40 are nuclear subunits and 9 are mitochondrial subunits. The mitochondrial complex I intermediate assembly (MCIA) complex is critical to the building of the membrane arm module, a system that has been lost in plants, suggesting the membrane arm subunits are assembled in an ancestral manner. Here, in this paper the author (Wang et al. 2022) characterize a new maize crumpled seed mutant, denoted as crp1 (crumpled kernel1). In developing seeds, CRP1 encodes an ortholog of human NDUFAF1 (NADH-ubiquinone oxidoreductase complex assembly factor 1), whose loss leads to a decrease in mitochondrial complex I, mitochondrial vacuolation, and changes in cellular energy. Further, ZmTIM17-1 and ZmIVD1, which are homologous to human TIMMDC1 and ACAD9, are also required for complex I activity and seed development. Anuradha Singh, 2022

Wang, G et al. 2022. An MCIA-like complex is required for mitochondrial complex I assembly and seed development in maize Molecular Plant.
   An MCIA-like complex is required for mitochondrial complex I assembly and seed development in maize
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Bo, C et al. 2022. Transcription factor ZmWRKY20 interacts with ZmWRKY115 to repress expression of ZmbZIP111 for salt tolerance in maize Plant J. :doi: 10.1111/tpj.15914.
   Transcription factor ZmWRKY20 interacts with ZmWRKY115 to repress expression of ZmbZIP111 for salt tolerance in maize

Soil hypersalinity is worsening globally and the accumulation of ions such as Na+ and Cl diminishes the ability of plants to absorb water, impairs metabolic processes such as photosynthesis, and inhibits growth. In addition, salt tolerance declines after wild plants are domesticated as crops. Therefore, it is critical to understand the mechanisms underlying the adaptation of crops to increases in soil salt content to restore and maintain high crop yield and quality. Maize is a glycophytic species that are sensitive to saline-alkaline stress. In maize, 119 WRKY genes have been classified based on bioinformatics, but the roles of other WRKY TFs, especially those in the network responding to salt stress, are still unclear. In this study, Bo et al. discovered a maize mutant wrky20 which exhibited a salt tolerance phenotype, including lower H2O2, MDA, and REL levels than B73 plants. Maize mutant wrky20 has a non-sense mutation from a glutamine (CAG) codon to a stop codon (TAG) at residue 298 in ZmWRKY20, which is responsible for the salt tolerance phenotype. By performing qRT-PCR, the researchers found that ZmWRKY20 was strongly expressed in the leaves and subtending leaves, and under NaCl stress, ZmWRKY20 expression gradually increased, reaching a maximum at 12 h and decreasing thereafter. In addition, they found that ZmWRKY20 is located in the nucleus, and the C-terminus contributed to the regulation of transcriptional activity of ZmWRKY20. To elucidate the functions of ZmWRKY20 in the salt stress response, they overexpressed ZmWRKY20 in WT maize and found that ZmWRKY20 overexpression increases salt stress sensitivity in maize. By comparing the transcriptome data from the leaves of stable ZmWRKY20-overexpressing and WT plants treated with and without 250 mM NaCl, they found that ZmbZIP111 was downregulated and its expression levels declined to a greater extent in the transgenic plants than in WT. Furthermore, they performed a yeast two-hybrid (Y2H) assay using ZmWRKY20 as bait and discovered that one of the target proteins interacting with ZmWRKY20-M1 was the nuclear group III WRKY TF family member named ZmWRKY115. Finally, the EMSA experiments confirmed that ZmWRKY20 and ZmWRKY115 independently bound a 52-bp sequence containing two different W-box elements of the ZmbZIP111 promoter in vitro. In summary, these findings improve our understanding of the complicated responses of maize to salt stress. Beibei Liu, 2022

Bo, C et al. 2022. Transcription factor ZmWRKY20 interacts with ZmWRKY115 to repress expression of ZmbZIP111 for salt tolerance in maize Plant J. :doi: 10.1111/tpj.15914.
   Transcription factor ZmWRKY20 interacts with ZmWRKY115 to repress expression of ZmbZIP111 for salt tolerance in maize
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Yuebin Wang et al. 2022. Three types of genes underlying the Gametophyte factor1 locus cause unilateral cross incompatibility in maize Nature communications. 13:4498.
   Three types of genes underlying the Gametophyte factor1 locus cause unilateral cross incompatibility in maize

Other sequences from inbred SK described: Zm00015a016198 (ZmGa1P.1); Zm00015a016199 (ZmGa1P.2); Zm00015a016201 (ZmGa1P.3); Zm00015a016206 (ZmGa1P.4); Zm00015a016210 (ZmGa1P.5); Zm00015a016192 (ZmPME4-1); Zm00015a016193 (ZmPME4-2); Zm00015a016197 (ZmPME4-3); Zm00015a016200 (ZmPME4-4); Zm00015a016203 (ZmPME4-5); Zm00015a016204 (ZmPME4-6); Zm00015a016209 (ZmPME4-7)

Common North American inbred lines used in research (B73, Mo17, W22) can accept pollen from each other without fertilization issues because they are all dent varieties of maize and contain the same type of Gametophyte factor1 (ga1) locus. Fertility issues can arise when crossing a popcorn by a dent corn variety, resulting in unilateral cross incompatibility (UCI) and no or reduced seed set. UCI is caused by the failure of the pollen tube to reach to ovule in a male/female ga1-dependent interaction. Wang et al. mapped the Ga1 locus and used segregation analysis to show that there are two components within the locus that affect fertility, then applied GWAS to find SNPs and candidate genes associated with Ga1. Several PECTIN METHYLESTERASE (PME), ZmGa1P, and ZmPRP genes were identified as associated with fertility and showed enrichment of gene expression in pollen or silks. Overexpression of these genes in UCI crosses resulted in an increase in fertility that was correlated with expression level, elucidating which genes affected either the male or female component of UCI. Finally, PCA using diverse inbred, landrace, and teosinte lines suggests that evolution of the Ga1 locus was occurring before maize domestication, with Z.mays ssp parviglumis leading to one type of Ga1 (ga1) and Zea mays ssp. Mexicana leading to the other two types of Ga1 (Ga1-S and Ga1-M). This research has resolved the Ga1 locus, which has been difficult to fine map due to large structural variation, identified candidate genes responsible for UCI, and provided evidence suggesting UCI was present in maize before domestication. Lander Geadelmann, 2022

Yuebin Wang et al. 2022. Three types of genes underlying the Gametophyte factor1 locus cause unilateral cross incompatibility in maize Nature communications. 13:4498.
   Three types of genes underlying the Gametophyte factor1 locus cause unilateral cross incompatibility in maize
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Li, Z et al. 2022. DeepBSA: A deep-learning algorithm improves bulked segregant analysis for dissecting complex traits Molecular Plant.
   DeepBSA: A deep-learning algorithm improves bulked segregant analysis for dissecting complex traits

As one of the most popular methods for mapping mutants and QTL, bulked segregant analysis (BSA) has been widely applied in animals and plants genetics studies. Especially with advances in next-generation sequencing, BSA has become a rapid and cost-effective method for dissecting complex traits. However, many factors influence the results of BSA. In this paper, the authors evaluated five major variables influencing the accurate detection of QTLs. They also developed a new BSA method driven by deep learning called deepBSA for QTL mapping and functional gene cloning. Their results suggest that DeepBSA is compatible with available bulked pools and performed well with various simulated and real datasets in animals and plants. DeepBSA outperformed all other algorithms when comparing absolute bias and signal-noise-ratio. They then used this method and fine mapped five maize QTLs, including three well-known plant-height genes. So they believe this method is easy to operate and can quickly map QTLs and functional genes. Lei Liu, 2022

Li, Z et al. 2022. DeepBSA: A deep-learning algorithm improves bulked segregant analysis for dissecting complex traits Molecular Plant.
   DeepBSA: A deep-learning algorithm improves bulked segregant analysis for dissecting complex traits
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Wang, XK, et al. 2022. Plant Physiol. 0:doi: 10.1093/plphys/kiac308
   Characterization of regulatory modules controlling leaf angle in maize

Leaf angle is an important agronomic feature in maize that impacts planting density and light penetration. A pair of classical transcription factors, ZmLG1 (liguleless1) and ZmLG2 (liguleless2), play important roles in ligular region formation which changes leaf angle. The authors found thatZmBEH1 (BZR1/BES1 homolog gene 1) is targeted by ZmLG2 and influences sclerenchyma cell layers on the adaxial side to regulate leaf angle formation. In addition, they showed that ZmBEH1 interacted directly with ZmBZR1 (Brassinazole Resistant 1), which was also directly activated by ZmLG2. Finally, ZmBEH1 and ZmBZR1 work synergistically on downstream targets such as ZmSCL28 (SCARECROW-LIKE 28) to regulate leaf angle in maize. This is one of the mechanistic studies that found three loci, ZmBZR1, ZmBEH1, and ZmSCL28 to be ideal targets for manipulating leaf angle to generate upright and semidwarf plant architecture. Anuradha Singh, 2022

ZmLG2 = Zm00001d042777 ZmBZR1 = Zm00001d021927 ZmBEH1 = Zm00001d046305 ZmSCL28 = Zm00001d045507

Wang, XK, et al. 2022. Plant Physiol. 0:doi: 10.1093/plphys/kiac308
   Characterization of regulatory modules controlling leaf angle in maize
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Gent, JI, et al. 2022. Plant Cell. 0:doi: 10.1093/plcell/koac199
   The maize gene maternal derepression of r1 encodes a DNA glycosylase that demethylates DNA and reduces siRNA expression in the endosperm

In this paper, the authors describe a DNA glycosylase that is homologous to DEMETER in arabidopsis. In Arabidopsis, DEMETER has been well studied and is known to be required for seed development, and has been linked to genomic imprinting. A mutant called mdr was discovered by Jerry Kermicle in 1978, and the authors mapped it to the tip of the long arm of chromosome 4, and were able to determine the mutation is a result of a deletion of one A in a string of seven A'a creating a frameshift mutation in dng101 (DNA glycosylase 101). Due to three additional genes in maize being DEMETER-like, the authors attempted to generate a double mutant of the two most highly endosperm expressed DEMETER-like genes but were unable to, suggesting that at least one of those two genes is required for seed development. The authors also investigated if this mutation affected endosperm demethylation because widespread demethylation in the endosperm is causative of genomic imprinted expression. To do this, they performed EM-seq and called differentially methylated regions in the endosperm then compared to previous imprinting calls and found a significant number of maternally expressed genes with overlapping differentially methylated regions. Additionally they evaluated the levels of siRNA present in WT and the mutant in both endosperm and embryo and found a striking change in the mutant endosperm when compared to WT. Finally, they found that DHH00002 family transposons that are maternally expressed are 2.5-fold more likely to overlap a differentially methylated region than endosperm expressed but non-imprinted DHH00002 family transposons. Kaitlin Higgins, 2022

Gent, JI, et al. 2022. Plant Cell. 0:doi: 10.1093/plcell/koac199
   The maize gene maternal derepression of r1 encodes a DNA glycosylase that demethylates DNA and reduces siRNA expression in the endosperm
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Li, CH, et al. 2022. Nature Plants. doi: 10.1038/s41477-022-01190-2
   Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding

It is still unknown whether the agronomic traits of female heterotic groups (FHGs) and male heterotic groups (MHGs) undergo different changes during the breeding history. In this study, Li et al. assembled 1604 maize inbred lines belonging to various heterotic groups, and conducted phenotyping and re-sequencing analyses. They found that FHGs and MHGs have undergone both convergent and divergent changes for different sets of agronomic traits. For example, the days to anthesis is reduced for both FHGs and MHGs, while ear diameter is reduced for FHGs and increased for MHGs. Selective signals and association analysis identified a large number of candidate genes controlling several important agronomic traits. Moreover, the authors observed increased genetic differentiation between FHGs and MHGs during breeding. The authors also validated the function of two selected genes and a differentiated gene. Taken together, this study provided deeper insights into the genetic basis of modern hybrid maize breeding. Hai Wang, 2022

Zm00001d010894 = ZmEMF1L1 Zm00001d025992 = ZmKW10 Zm00001d039284 = ZmKOB1

Li, CH, et al. 2022. Nature Plants. doi: 10.1038/s41477-022-01190-2
   Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding
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Zhang, M, et al. 2022. New Phytol. 0:doi: 10.1111/nph.18317
   miR169o and ZmNF-YA13 act in concert to coordinate the expression of ZmYUC1 that determines seed size and weight in maize kernels

MicroRNAs (miRNAs) are a class of small non-coding RNAs enriched in about 21 nucleotides (nt) which can regulate gene expression at the post-transcriptional level. miRNAs play key regulatory roles in seed development and emerge as new key targets for engineering grain size and yield. The Zma-miRNA169 family is highly expressed during maize seed development, but its functional roles in seed development remain elusive. In this study, by investigating transgenic maize, Zhang et al. found that overexpression of maize miRNA zma-miR169o increases seed size and weight by promoting cell proliferation in the central endosperm, whereas the opposite is true when its expression is suppressed. To determine the molecular mechanism underpinning zmamiR169's regulation in seed size, the potential targets of zma-miR169 were predicted by using psRNA Target. Further studies revealed that zmamiR169 can negatively regulate its target gene, a transcription factor ZmNF-YA13 that also plays a key role in determining seed size. Plant hormones are important factors in regulating cell division and expansion. The proliferation and differentiation of maize seeds are mainly regulated by auxin and cytokinin in concert. By measuring the auxin and cytokinin contents in 5 DAP kernels, they illustrated that ZmNF-YA13 regulates the expression of the auxin biosynthetic gene ZmYUC1, which modulates auxin levels in the early developing seeds and determines the number of endosperm cells, thereby governing maize seed size and ultimately yield. Overall, this study has demonstrated that zma-miR169o and ZmNF-YA13 can form a functional module regulating auxin accumulation in maize seeds and playing an important role in determining maize seed size and yield, providing a set of novel molecular tools for yield improvement in molecular breeding and genetic engineering. Beibei Liu, 2022

Zhang, M, et al. 2022. New Phytol. 0:doi: 10.1111/nph.18317
   miR169o and ZmNF-YA13 act in concert to coordinate the expression of ZmYUC1 that determines seed size and weight in maize kernels
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. 2022. PLoS One. 17:10.1371/journal.pone.0269374
   Measurements of the number of specified and unspecified cells in the shoot apical meristem during a plastochron in rice (Oryza sativa) reveal the robustness of cellular specification process in plant development

The shoot apical meristem (SAM) is the pool of stem cells from which leaves are initiated. SAM morphology and dynamics are thought to be largely conserved between rice and maize, with many genes showing similar expression patterns and functions. One such gene is KNOTTED1/OSH1, in maize and rice respectively, whose protein accumulates in undifferentiated cells. Nosaka-Takahashi et al. used this fact to determine if the number of cells that differentiate into leaves was altered in mutants with altered meristem size. Some mutants in maize and rice that have altered meristem size have altered leaf initiation patterns, or phyllotaxy. To achieve this, they used a dual-staining technique on serial sections. One stain shows OSH1 protein with a secondary fluorescent reporter, and a second stain with propidium iodide shows nuclei. This allows for the counting of undifferentiated cells (OSH1-positive) and differentiated cells (OSH1-negative) when the images are overlayed. They find that in SAM size mutants, the number of undifferentiated cells is altered, but the number of cells that differentiate to leaf primordia stays the same. This demonstrates the robustness of leaf initiation, regardless of the morphology of the SAM. A continuing challenge in maize is the construction of a KNOTTED1 reporter. Assuming conserved biology between rice and maize SAMs, it is possible maize also has similar robust leaf initiation mechanisms. A following question, however, is does this remain true in meristem mutants that alter phyllotaxy such as abph1, or mutants with altered leaf dimensions? Lander Geadelmann, 2022

. 2022. PLoS One. 17:10.1371/journal.pone.0269374
   Measurements of the number of specified and unspecified cells in the shoot apical meristem during a plastochron in rice (Oryza sativa) reveal the robustness of cellular specification process in plant development
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Shaw, A, et al. 2021. PLoS One. 16:10.1371/journal.pone.0259710
   Differential retention contributes to racial/ethnic disparity in U.S. academia

The authors of this study used 25 years of publicly-available data from the National Science Foundation to predict racial and ethnic representation through the academic pipeline (starting at the undergraduate level), assuming no racial/ethnic bias in retention from one step to the next. The authors compared these predictions to the actual values for each racial and ethnic group under study. Their model suggests that White scholars are overrepresented at each next step in the academic pipeline from the postdoctoral level onward. Individuals from all other groups were underrepresented, but Black & African American, American Indian & Alaskan Native, and Native Hawaiian & Pacific Islander scholars showed the largest losses in predicted representation. This paper reinforced what we already know about misrepresentation in recruitment, particularly at the undergraduate level. It added an additional view of where retention efforts are failing. The data in this paper also indicate that retention efforts do not affect all groups equally. Efforts to increase retention throughout the academic pipeline need to be tailored to the experiences, cultures, and identities of the individuals making it up. Tessa Durham Brooks, 2022

Shaw, A, et al. 2021. PLoS One. 16:10.1371/journal.pone.0259710
   Differential retention contributes to racial/ethnic disparity in U.S. academia
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Han, TW et al. 2021. An epigenetic basis of inbreeding depression in maize Science. 7:eabg5442.
   An epigenetic basis of inbreeding depression in maize

Other genes whose expression was measured via DAP-qPCR: Zm00001d029983 Zm00001d044353

In this study the authors found that CHH hypermethylation often occurs during inbreeding in regions spanning TCP binding sites. The downregulation caused by the increased methylation was linked to the reduced binding affinity of regulatory proteins and ultimately led to reduced vigor in the developing plants. To study this, they used F1 hybrids that were self pollinated until the sixth generation, after which they selfed one plant and used single seed descent through the S11 generation. Additionally during the S10 generation, they randomly mated 25 lines to make a random mating population (M11). The comparison of the two groups (S11, and M11) with several growth phenotypes was consistent with known affects of inbreeding. The genomic uniformity between lines suggested the phenotypic variation could be attributable to something other than genetic code. Using methyl-seq the authors explore the differences in the epigenomes of the inbred and randomly mated populations to determine causes of the phenotypic variation and found that CHH hypermethylation across the TCP binding sites reduced chromatin accessibility and reduced transcription of those genes. All in all, this is a wonderful example of the impact the epigenome can have on phenotype. Kaitlin Higgins, 2022

Han, TW et al. 2021. An epigenetic basis of inbreeding depression in maize Science. 7:eabg5442.
   An epigenetic basis of inbreeding depression in maize
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Zhou, XY, et al. 2022. New Phytol. 0:doi: 10.1111/nph.18278
   The classical SOS pathway confers natural variation of salt tolerance in maize

The excessive uptake of Na+ causes salt stress in plants, which impacts a variety of physiological processes. Na+ regulation via the Salt Overly Sensitive (SOS) pathway in Arabidopsis has been extensively studied and is composed of three proteins: SOS3 (a Ca2+ binding protein from the CBL family), SOS2 (a protein kinase from the CIPK family), and SOS1 (a plasma membrane Na+/H+ antiporter from the NHX family), but it is still poorly understood in Zea mays. The authors of this paper have previously screened ~500 inbred lines and observed a salt hypersensitive phenotype along with reduced biomass in the LH65 line. This phenotype was then examined genetically, and it was found to be linked to a single recessive gene (Salt Tolerance Locus 2, ZmSTL2). An association with salt hypersensitivity caused by ZmSTL2 is a natural frameshifting deletion in the coding region of ZmSOS1. Consequently, they demonstrated and validated that ZmSOS1 is activated by the maize SOS3/SOS2 complex through phosphorylation of ZmCBL4 and ZmCBL8, and mutants lacking these proteins display defected Na+ regulation and salt hypersensitivity. Finally, they state that the classical SOS pathway (ZmSOS1 and ZmCBL8) confers the diversity of Na+ regulation and salt tolerance in maize, suggesting potential gene targets for developing salt-tolerant maize. Anuradha Singh, 2022

Zhou, XY, et al. 2022. New Phytol. 0:doi: 10.1111/nph.18278
   The classical SOS pathway confers natural variation of salt tolerance in maize
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Simaskova, M, et al. 2022. Plant Cell. 0:doi: 10.1093/plcell/koac151
   KIL1 terminates fertility in maize by controlling silk senescence

Flowers are receptive to pollination during a limited window, which varies from mere hours to weeks. After the pollination period, age-induced senescence of unpollinated flowers occurs, thus ending the potential for flowers to produce seeds and fruits. In maize, silk strands are the elongated floral stigmas that emerge from the husk-enveloped inflorescence to intercept airborne pollen. Silk senescence has been previously described on a morphological basis, but its molecular regulation remains largely unknown. In this study, Simaskova et al. investigated the functions of programmed cell death (PCD) in regulating maize silk senescence. First, they found a negative correlation between inflorescence age and the potential of ovaries to become fertilized and develop into kernels, which is caused by the tissue degeneration of the basal ovary-proximal area of silk strands. By conducting histological and microscopy analysis, they revealed that cellular features of PCD precede silk base degeneration. The importance of transcriptional regulation for the initiation of senescence and developmental PCD in plants has been demonstrated in several systems. To identify candidate transcriptional regulators of silk senescence, they analyzed changes in gene expression in senescent silk strands and discovered several induced transcription factor genes in this tissue. Using transfected maize mesophyll protoplasts and N. benthamiana leaf, they demonstrated that KIL1 is a potent PCD activator. To further investigate the function of KIL1, they generated transgenic maize lines (overexpressing/silencing KIL1 in maize) and found that overexpression of KIL1 leads to a precocious termination of silk receptivity in maize, while kil1 loss-of-function mutants show delayed silk senescence and extended silk receptivity. Finally, by analyzing the RNA-seq from the silk bases of KIL1-OE, KIL1-SRDX lines, and the WT at 11 DASE, they demonstrated that KIL1 regulates the senescence-induced PCD by transcriptional activation of downstream genes. In summary, the discovery of this research provides us with more new insights into the modulation of maize fertility and offers unique opportunities for possibly improving yield stability in cereal crops. Beibei Liu, 2022

KIL1 (KIRA1-Like1) = nactf36 - NAC-transcription factor 36 =Zm00001eb077580

Simaskova, M, et al. 2022. Plant Cell. 0:doi: 10.1093/plcell/koac151
   KIL1 terminates fertility in maize by controlling silk senescence
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Wang, YY, et al. 2022. Nature communications. 13:2222
   A dirigent family protein confers variation of Casparian strip thickness and salt tolerance in maize

Wang et al. screened about 200 maize inbred lines for their response under different transpiring conditions and salt stress response. From the screen, authors found salt tolerant 3H-2 and sensitive CIMBL45 inbred lines. Through the bulked segregant analysis (BSA), they have found the causal gene which encodes a dirigent family protein and named it as ZmSTL1 (Salt-Tolerant Locus1). The identification of ZmSTL1 was further confirmed by CRISPR-Cas9 allele under the salt stress condition. Interestingly, ZmSTL1 falls into the same phylogenetic group of known Arabidopsis AtESBL (Enhanced Suberin Like) and further renamed as ZmSTL1/ZmESBL. Cellular studies suggest that ZmESBL is localized in the Casparian domain and ZmESBLcrispr mutants demonstrate aberrant Casparian strips due to incomplete lignin deposition. Furthermore, authors demonstrated that ZmESBL-dependent Casparian strips provide barriers for the sodium ion to the stele. This study provided the comprehensive idea about the importance of Casparian strips during salt stress in maize. Arif Ashraf, 2022

Wang et al. screened about 200 maize inbred lines for their response under different transpiring conditions and salt stress response. From the screen, authors found salt tolerant 3H-2 and sensitive CIMBL45 inbred lines. Through the bulked segregant analysis (BSA), they have found the causal gene which encodes a dirigent family protein and named it as ZmSTL1 (Salt-Tolerant Locus1). The identification of ZmSTL1 was further confirmed by CRISPR-Cas9 allele under the salt stress condition. Interestingly, ZmSTL1 falls into the same phylogenetic group of known Arabidopsis AtESBL (Enhanced Suberin Like) and further renamed as ZmSTL1/ZmESBL. Cellular studies suggest that ZmESBL is localized in the Casparian domain and ZmESBLcrispr mutants demonstrate aberrant Casparian strips due to incomplete lignin deposition. Furthermore, authors demonstrated that ZmESBL-dependent Casparian strips provide barriers for the sodium ion to the stele. This study provided the comprehensive idea about the importance of Casparian strips during salt stress in maize. Arif Ashraf, 2022

Gene: ZmSLT1/ZmESBL = Zm00001d033942

Wang, YY, et al. 2022. Nature communications. 13:2222
   A dirigent family protein confers variation of Casparian strip thickness and salt tolerance in maize
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Kretschmer , M, et al. 2022. Science. 376:1187-1191
   Organic acids and glucose prime late-stage fungal biotrophy in maize

Plant-associated fungi depend on living hosts to proliferate, but the molecular basis of how the plant facilities the biotrophic lifestyle of fungi is still unknown. In this Science paper, Prof. James Kronstad's group reported that malate and glucose are two important metabolites to stimulate maize fungal pathogen Ustilago maydis cell proliferation, increase culture viscosity, and trigger the accumulation of dark, pigmented cells. Maize carries out C4 photosynthesis of the NADP malic enzyme subtype in which 75% of CO2 is initially fixed into malate, and the authors hypothesized that metabolic adaptation to organic acids is a key determinant of biotrophic proliferation for U. maydis. The authors also knock out dicarboxylate transporters, which may function in organic acids transportation. They found that deletion of both jen2 and jen20 attenuated virulence in maize. Therefore, they proposed that the response to defined combinations of nutrients may therefore be a general theme in plant-microbe interactions. Lei Liu, 2022

Obligate biotrophs depend on living hosts to proliferate, but the molecular basis of such phenomenon is still obscure. In this study, using the Ustilago maydis and maize as the model system, Matthias et al. identified organic acids and glucose as the main carbon sources to induce late-stage fungal biotrophy. Maize is a C4 plant species belonging to the NADP malic enzyme subtype. In maize, 75% of CO2 is initially fixed into malate, thus the authors hypothesized that organic acids might be a key determinant of biotrophic proliferation for U. maydis. Indeed, when cultured on glucose and malate, enhanced cell proliferation, as well as over-accumulation of extracellular poly-saccharide and melanin, was observed for U. maydis. It has been previously reported that Melanin formation during U. maydis sporulation in tumors is catalyzed by the laccase Lac1 and the polyketide synthase Pks1. Consistent with this, transcriptome analysis revealed that glucose and malate together could induce Pks expression, and the induction was dependent on two transcription factor genes, Mtf1 and Unh1. The importance of organic acids for biotrophy was further confirmed by the finding that knocking out two dicarboxylate transporters jeopardized the virulence of U. maydis on maize. In addition, organic acids induce the expression of effectors characteristic of biotrophic development. Moreover, the authors revealed an important role of mitochondrial functions and oxygen sensing in organic acid-induced biotrophic development. Taken together, this study depicts a complex response of U. maydis to organic acids that involves mitochondrial functions, oxygen sensing, carboxylate transporters, and transcriptional regulators of traits related to biotrophy. Hai Wang, 2022

Kretschmer , M, et al. 2022. Science. 376:1187-1191
   Organic acids and glucose prime late-stage fungal biotrophy in maize
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Handelsman, J, et al. 2022. Science. 0:1057-1059
   Achieving STEM diversity: Fix the classrooms

Among the avenues of promoting equity in STEM is the inclusion, involvement, and retention of college students from diverse backgrounds. However, diverse barriers exist that slow progress. In this recent policy paper, Handelsman et al. (2022) discuss ways of handling intricate barriers at the classroom level that hinder enrollment and retention of college students from historically excluded communities (HECs). They highlight different ways instructors, leaders, and government agencies can create inclusive STEM college classrooms; through teaching practices, class environment/instructor expectations, and class content. The article is interesting as it reiterates the importance of building diversity in STEM beginning early in college and puts into perspective some additional efforts required at the classroom level to attract and retain students from HECs in STEM. Andrew Egesa, 2022

Handelsman, J, et al. 2022. Science. 0:1057-1059
   Achieving STEM diversity: Fix the classrooms
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Baldauf, JA, et al. 2022. Plant Physiol. 0:doi: 10.1093/plphys/kiac180
   Single-parent expression complementation contributes to phenotypic heterosis in maize hybrids



Heterosis, or hybrid vigor, is a critical component of modern agricultural, yet deep understanding of mechanisms behind heterosis remain elusive. The complementation or dominance model of heterosis hypothesizes deleterious alleles within a maize inbred are complemented with beneficial alleles in an F1 hybrid. Single-parent expression (SPE) is an example of this, where the "deleterious" allele is absent in one parent and a functional "beneficial" allele is present in the other parent of a hybrid. The objective of Balduf et al. was to examine SPE complementation in heterotic traits and how gene co-expression networks connect SPE with phenotypes. Three tissue types from six inbred lines and their hybrids with B73 were collected: the flag leaf, meiotic tassel, and immature ear. Root expression data was brought in from previous studies for organ-level SPE analysis. In examining SPE expression patterns, non-syntenic genes to sorghum were enriched among SPE genes. Additionally, a correlation between the number of SPE genes and the heterotic increase of certain traits was detected. Applying WGCNA analysis revealed SPE expression patterns could be separated by correlation, and that hybrids had expression modules that more closely resembled that of on parent's expression pattern. Interestingly, when connecting these modules with phenotypic traits, modules enriched in B73 SPE were positively correlated with heterotic traits, whereas the opposite was true of other inbred lines. This work furthers our genomic understanding of heterosis and enhances the evidence of the complementation/dominance model of heterosis. Lander Geadelmann, 2022

Baldauf, JA, et al. 2022. Plant Physiol. 0:doi: 10.1093/plphys/kiac180
   Single-parent expression complementation contributes to phenotypic heterosis in maize hybrids
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Zhuoyang Li et al. 2022. The transcription factor bZIP68 negatively regulates cold tolerance in maize Plant Cell. 34:2833-2851.
   The transcription factor bZIP68 negatively regulates cold tolerance in maize

Cold stress is a major environmental threat to the growth, development, and geographical distribution of crops in nature. The wild ancestor of maize, teosinte, originated from tropical and subtropical areas, which caused teosinte to be susceptible to low temperatures. However, domesticated maize can be planted from hot tropical to cold temperate, suggesting modern maize acquired the cold-resistant ability. In this article, Li et al. characterized that a bZIP gene, bZIP68, controls the maize adoption to cold environments. The overexpression lines of bZIP68 showed more susceptibility to cold, and knock-out lines became resistant to cold. The bZIP68 locus was found as a target of selection during early domestication, and its promoter has a 358-bp InDel and significantly affects the differential expression of bZIP68 between maize and teosinte. This article uncovered an evolutionary cis-regulatory variant that could be used to improve cold tolerance in maize. Lei Liu, 2022

bZIP68 = Zm00001d050018

Cold stress is a majorZea mays) is a major food crop that has adapted to a wide range of environmental conditions worldwide. However, because it originated in tropical latitudes, maize is more susceptible to cold stress than other cereal crops. Therefore, it is important to elucidate the mechanism that regulates cold sensitivity in maize, which will enable us to introduce key cold-tolerance genes/modules from other species for breeding cold-tolerant maize varieties. Here, Li et al. identified bZIP68, a basic leucine zipper (bZIP) transcription factor, as a negative regulator of cold tolerance in maize at both germination and seedling stages by screening a previously described population of transgenic maize plants overexpressing more than 700 maize genes. By performing yeast two-hybrid assay and in vitro kinase assay, they found that MPK8 can control the stability and transcriptional activity of bZIP68 by phosphorylation at the conserved Ser250 residue of Bzip68 under cold stress. To identify the potential target genes of bZIP68 that are responsible for the cold response, they generated transcriptome deep sequencing data and found that bZIP68 represses the cold-induced expression of DREB1 transcription factor genes by directly binding to its promoter. Furthermore, by performing HITAC-seq and nucleotide diversity analysis, they demonstrated that the bZIP68 locus was a target of selection during early domestication. A 358-bp insertion/deletion (Indel-972) polymorphism in the bZIP68 promoter has a significant effect on the differential expression of bZIP68 between maize and its wild ancestor teosinte. This study thus uncovered an evolutionary cis-regulatory variant that could be used to improve cold tolerance in maize. Beibei Liu, 2022

Zea mays is susceptible to low temperature stress. In this study, Li et al. identified one basic leucine zipper transcription factor, bZIP68, as one of the negative regulators of cold tolerance in maize. Using Y2H, BiFC, and co-immunoprecipitation experiment, authors have found that MPK8 (MITOGEN-ACTIVATED PROTEIN KINASE 8) not only physically interacts with bZIP68, but also phosphorylates bZIP68 at conserved Ser250 residue. This phosphorylation event enhances the bZIP68 protein stability and binding capacity with DREB1.7 promoter during low temperature stress. Interestingly, Li et al. found that bZIP68 locus went through selection during the maize domestication, where 358 bp insertion/deletion region was identified. This study provides the opportunity to engineer evolutionary important locus for creating low temperature stress tolerant maize varieties in near future. Arif Ashraf, 2022

Sequence data from this article can be found in the GenBank/EMBL libraries under the following accession num- bers: bZIP68 (NP_001353894, Zm00001d050018); MPK8 (NP_001149495, Zm00001d014658); bZIP49 (XM_008666300, Zm00001d031790); bZIP123 (NM_001136667, Zm00001d Downloaded from https://academic.oup.com/plcell/article/34/8/2833/6584020 by University of Massachusetts/Amherst user on 18 August 2022 bZIP68 regulates cold tolerance in maize THE PLANT CELL 2022: 34; 2833–2851 | 2849 005884); bZIP4 (XM_008658809, Zm00001d012294); DREB1.1 (XM_008672111, Zm00001d006169); DREB1.2 (NM_001146 976, Zm00001d021205); DREB1.3 (XM_008654734, Zm00001 d021208); DREB1.4 (NM_001159200, Zm00001d006170); DRE B1.5 (XM_020541212, Zm00001d021207); DREB1.7 (NM_001 177010, Zm00001d036003); DREB1.10 (NM_001154158, Zm0 0001d002618); ZmMPK11 (XP_008656705, Zm00001d 011465); ZmNF-YB10 (NP_001130166, Zm00001d050242). Ubi-2 (NM_001329666, Zm00001d053838); AtABF2 (NP_84 9777, AT1G45249); OsTRAB1 (NP_001390561, Os08t047 2000). RNA-seq data are available at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/) under series entry PRJNA778546, which can be downloaded at http://www.ncbi.nlm.nih.gov/sra/PRJNA778546.

Zhuoyang Li et al. 2022. The transcription factor bZIP68 negatively regulates cold tolerance in maize Plant Cell. 34:2833-2851.
   The transcription factor bZIP68 negatively regulates cold tolerance in maize
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Ding, RS, et al. 2022. Plant Cell Environ. 0:doi: 10.1111/pce.14358
   Plasticity in stomatal behavior across a gradient of water supply is consistent among field-grown maize inbred lines with varying stomatal patterning

Plants employ stomata to regulate the exchange of carbon and water between themselves and the environment. The stomatal conductance (gs) of a plant is crucial and can be modeled by Ball-Berry (BB) and Medlyn (MED) models. The slope parameter varied across species and across models, such as the BB index (m) and the MED index (g1). To model BB and MED parameters, gs were measured using four different maize genotypes (B73, MS71, RIL1, and RIL2). Significant differences exist among the four maize inbred lines studied when it comes to stomatal density, stomatal patterning and anatomy, and A and gs. Regardless, their m and g1 were highly similar. Furthermore, there was no evidence of genotype-specific plasticity in m or g1 in response to a water supply gradient. Because the gs-model parameter values are consistent across genotypes, the structure-function links between stomatal patterning and other aspects of leaf gas exchange must be somewhat variable. Anuradha Singh, 2022

Ding, RS, et al. 2022. Plant Cell Environ. 0:doi: 10.1111/pce.14358
   Plasticity in stomatal behavior across a gradient of water supply is consistent among field-grown maize inbred lines with varying stomatal patterning
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Montgomery, BL et al. 2022. The roots of change: cultivating equity and change across generations from healthy roots Oxf Surv Plant Mol Cell Biol. 0:https://doi.org/10.1093/plcell/koac121.
   The roots of change: cultivating equity and change across generations from healthy roots

Professional organizations and disciplinary societies have established mechanisms and structures to support equity and inclusion, and have committed to addressing Diversity, Equity, and Inclusion (DEI) matters. In this letter to the editor, the authors reflect on these mechanisms and structures, how these structures are evolving, associated controversies, responses to these structures and evident challenges to their success, such as existing resistance to change and unsuitable organizational structures and practices. More importantly, they describe diverse avenues of supporting the DEI mechanisms. This article is interesting because it describes efforts in supporting DEI structures, it also highlights some of the challenges facing existing DEI structures that societies should reflect on. Andrew Egesa, 2022

Montgomery, BL et al. 2022. The roots of change: cultivating equity and change across generations from healthy roots Oxf Surv Plant Mol Cell Biol. 0:https://doi.org/10.1093/plcell/koac121.
   The roots of change: cultivating equity and change across generations from healthy roots
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Lin, M, et al. 2022. Plant Physiol. 0:doi: 10.1093/plphys/kiac198
   Integrating GWAS and TWAS to elucidate the genetic architecture of maize leaf cuticular conductance

Other candidate genes identified for leaf cuticular conductance (gc): Zm00001d012964 Zm00001d022364 Zm00001d032788 Zm00001d012175 Zm00001d036765 Zm00001d038404 Zm00001d038405 Zm00001d040788 Zm00001d029141 Zm00001d042612

Water loss in the leaf is mostly mediated by stomata. Apart from stomata-mediated water loss, when stomata are closed at night, cuticular wax at the epidermal cell layer prevents water loss. In this study, Lin et al. utilized 310 maize inbred lines to perform the GWAS and TWAS (Transcriptome-wide association studies). Additionally, authors quantified cuticular composition and structure of 51 inbred lines based on the highest and lowest leaf cuticular conductance (gc). Analyzing their GWAS and TWAS data, Lin et al. narrowed down some potential candidate genes, involved in cuticle biosynthesis and export (GDSL lipase, KCS3, CER3-like, CER5-like), cell wall modification (PME40, PAE5), intracellular membrane trafficking (SEC15B, ISTL1, Ypt/Rab-GAP, a1-COP, SNARE, SEC14), and regulator of cuticle development (GLK35, WRKY64, MYB108, CER9, MIEL1-like, MYB54, GLK35, CER7). This study helped to identify a list of candidate genes involved in leaf cuticular conductance, which will facilitate the future functional characterization of individual genes. Arif Ashraf, 2022

Genes in this paper: MIEL1-like (Zm00001d029141), GDSL esterase/lipase (Zm00001d032788), MYB54 (Zm00001d002843), GLK35 (Zm00001d005087), a1-COP (Zm00001d039411), SEC15B (Zm00001d040788), CER7 (Zm00001d042612), PME40 (Zm00001d043509), WRKY64 (Zm00001d044162), KCS3 (Zm00001d048953), ISTL1 (Zm00001d049479), MYB108 (Zm00001d050185), Rab-GAP/TBC (Zm00001d051599), SEC14 (Zm00001d012964), CER3-like (Zm00001d015477), CER9 (Zm00001d036765), Ypt/Rab-GAP (Zm00001d038404), SNARE (Zm00001d022364), CER5/ABCG12-like (Zm00001d010426), PAE5 (Zm00001d012175), Ypt/Rab-GAP (Zm00001d025180) Arif Ashraf, 2022

Lin, M, et al. 2022. Plant Physiol. 0:doi: 10.1093/plphys/kiac198
   Integrating GWAS and TWAS to elucidate the genetic architecture of maize leaf cuticular conductance
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Zhang, JH, et al. 2022. J Integr Plant Biol. 0:doi: 10.1111/jipb.13254
   Ascorbate peroxidase 1 confers resistance to southern corn leaf blight in maize



Southern corn leaf blight (SCLB), caused by Bipolaris maydis, is a devastating disease of maize, but the genetic basis of maize resistance against SCLB is still unclear. In this study, Zhang et al. compared the proteome of B.maydis-inoculated Mo17 with that of mock-inoculated Mo17 by TMT6, leading to the identification of 258 differentially abundant proteins. Among them, ascorbate peroxidase 1 (ZmAPX1) was found within a previously reported QTL associated with maize resistance to SCLB. To test whether ZmAPX1 modulated SCLB resistance, the authors overexpressed ZmAPX1 and found that these overexpressors accumulated lower ROS and exhibited enhanced resistance against B.maydis. The authors further identified JA-signaling pathway as a possible component of ZmAPX1-mediated resistance, as JA levels and JA-related genes were found up-regulated in ZmAPX1-overexpressors infected with B.maydis, whereas Zmapx1 mutants showed the opposite effects. Taken together, this study identified ZmAPX1 as a positive regulator of maize resistance against SCLB. Although it's still unclear whether natural variation of ZmAPX1 at least partly explains maize phenotypic diversity in SCLB resistance, engineering of ZmAPX1 may provide a feasible approach to enhance maize SCLB resistance in the future. Hai Wang, 2022

Zhang, JH, et al. 2022. J Integr Plant Biol. 0:doi: 10.1111/jipb.13254
   Ascorbate peroxidase 1 confers resistance to southern corn leaf blight in maize
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Wang, ZP, et al. 2022. J Integr Plant Biol. 0:doi: 10.1111/jipb.13263
   Efficient and genotype independent maize transformation using pollen transfected by DNA-coated magnetic nanoparticles

Genetic transformation in maize by traditional methods was time-consuming, labor-intensive and expensive. Moreover, genetic transformation can only be achieved successfully in a few genetic background, making it difficult to genetically modify elite germplasm widely used in maize breeding programs. An alternative tissue culture-independent method, ferroferric oxide (Fe3O4) magnetic nanoparticles (MNPs)-mediated pollen transfection, was formerly applied on cotton (Zhao et al., 2017, Nature Plants), but was later reported to be irreproducible by another study (Vejlupkova et al., 2020, Nature Plants). In this study, the authors reported successful application of MNPs-mediated pollen transfection in maize. Pollen was pretreated to open the germination aperture to enhance the efficiency of DNA entry, and transfection was performed at a cool temperature to maintain high pollen viability. MNPs coated with DNA encoding RFP, GUS, eGFP or Bar was delivered into pollen grains, which was used to pollinate female florets of maize. RFP was detected in 22% transfected pollen grains, GUS straining was observed in 55% embryos, and eGFP was detected in silk filaments and immature kernels. In the T1 generation, the authors observed plants with reporter gene transcripts and proteins at high rates, confirming that the transgene was integrated into the maize genome and can be passed to the next generation. This study demonstrated the feasibility of pollen transfection in genotype-independent maize genetic transformation. Hai Wang, 2022

Wang, ZP, et al. 2022. J Integr Plant Biol. 0:doi: 10.1111/jipb.13263
   Efficient and genotype independent maize transformation using pollen transfected by DNA-coated magnetic nanoparticles
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Kersaint, G, et al. 2022. Frontiers in Education. 0:https://doi.org/10.3389/feduc.2021.755471
   The Influence of Professional Engineering Organizations on Women and Underrepresented Minority Students' Fit

This article investigates the role of professional bodies in supporting students and early career professions in Engineering using cultural models of engineering success (CMES). It describes how professional bodies can influence, support, and equip women and underrepresented minorities in engineering. The authors conducted a longitudinal study in which they interviewed women in engineering and students from diverse backgrounds, early in their studies especially on mentorship and participation in professional bodies. The paper discusses factors to participatory decision-making and the benefits of belonging to the professional bodies while reemphasizing the critical role of professional bodies in building capacity and support for women and underrepresented minorities in professional communities. I find the paper an interesting read since it points out how underrepresented minorities benefit from being members of professional bodies and informs us to refocus our professional bodies to offer much of the needed support to early career professionals from minority backgrounds in their professional journeys. Andrew Egesa, 2022

Kersaint, G, et al. 2022. Frontiers in Education. 0:https://doi.org/10.3389/feduc.2021.755471
   The Influence of Professional Engineering Organizations on Women and Underrepresented Minority Students' Fit
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Li, W; Chen, YD; Wang, YL; Zhao, J; Wang, YJ. 2022. Plant J. 0:doi: 10.1111/tpj.15748
   Gypsy retrotransposon-derived maize lncRNA GARR2 modulates gibberellin response

Long non-coding RNAs (LncRNAs) are transcripts greater than 200 nucleotides that show poor protein-coding capacity. LncRNAs are involved in multiple biological processes, including gene expression, RNA processing, and chromatin remodeling. The plant hormone gibberellin (GA) orchestrates diverse aspects of biological events, from seed dormancy and germination, plant height determination, and floral organ morphogenesis to fruit senescence. However, the regulatory hierarchy of lncRNAs governing the GA response in crops remains largely elusive. In this research, Li et al., constructed eight strand-specific and ribosomal-depleted RNA libraries for RNA sequencing (RNA-seq) by using the second leaf sheath of Dwarf11 (D11) and maize inbred line Mo17 treated with water and 104 M GA��������3��. Four GIBBERELLIN-RESPONSIVE lncRNAs (GARRs) were found to be differentially expressed in both GA treated WT and D11 leaf sheaths compared with their water-treated counterparts. Among these 4 GARRs, only one GARR (GARR2) with a length of 2809 bp matched with the B73 reference sequence. Further analysis demonstrated that GARR2 was derived from a Gypsy LTR retrotransposon and GA-responsive element P-boxes were identified upstream of GARR2. To validate the involvement of GARR2 in the GA response in maize, Li et al., edited GARR2 by the CRISPR/Cas9 method. It was found that GARR2KO leads to increased shoot height, a longer second leaf sheath, and higher endogenous GA3 levels, reminiscent of a GA-induced phenotype. Furthermore, to characterize the GARR2-mediated regulatory network, they revealed the transcriptomic dynamics of GARR2 through RNA-seq analyses of WT and GARR2KO. It was found that the editing of GARR2 resulted in changes in the transcriptional abundance of GA pathway components and endogenous GA contents. Besides GA, GARR2 affected the primary auxin response. Finally, to identify proteins associated with GARR2, they performed RNA pull-down assays, which revealed that the HECT ubiquitin-protein ligase family member ZmUPL1 is a potential interaction target of GARR2. In summary, the results of this article provide some important insights into how lncRNA governs the GA response to affect the development and growth of maize. Beibei Liu, 2022

Li, W; Chen, YD; Wang, YL; Zhao, J; Wang, YJ. 2022. Plant J. 0:doi: 10.1111/tpj.15748
   Gypsy retrotransposon-derived maize lncRNA GARR2 modulates gibberellin response
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Hughes, TE; Langdale, JA. 2022. Development. 0:doi: 10.1242/dev.200410
   SCARECROW is deployed in distinct contexts during rice and maize leaf development

SCARECROW (SCR) transcription factor is well studied for its role in root development. But the role of SCR during the developmental context other than root is not well known. In this article, Hughes et al. explored the role of SCR for stomatal development in rice and maize. Although in Arabidopsis, there is single copy of SCR, but both rice (OsSCR1, OsSCR2) and maize (ZmSCR1, ZmSCR1h) have two copies of SCR. CRISPR-Cas9 knockout mutant of rice SCR (Osscr1;Osscr2) produces very small numbers of stomata. Further experiment suggests that expression of OsMUTE is reduced in Osscr1;Osscr2. This indicates the early-stage regulation during stomatal by OsSCR1 and OsSCR1. In contrast to dramatic stomatal phenotype in rice, there is a reduction of adaxial stomatal density for zmscr1;zmscr1h mutant in maize. This study highlights the diverse developmental role of SCR between rice and maize. Arif Ashraf, 2022

ZmSCR1 = GRMZM2G131516

ZmSCR1h = GRMZM2G015080

Hughes, TE; Langdale, JA. 2022. Development. 0:doi: 10.1242/dev.200410
   SCARECROW is deployed in distinct contexts during rice and maize leaf development
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Chen, WK, et al. 2022. Science. 375:DOI: 10.1126/science.abg7985
   Convergent selection of a WD40 protein that enhances grain yield in maize and rice

Most crops were domesticated from their wild ancestor within the past 12 000 years. During domestication and improvement, people chose what they needed for living which led to the pyramiding of beneficial mutations and recombinants in key genes and caused many different crop species to share common domesticated traits. Kernel or grain number determines the crop yield, and underwent strong selection during crop domestication. For maize, its wild ancestor teosinte only has 6-12 kernels on the ear, while modern maize hybrid can harbor over 500 kernels on the ear, which is mainly caused by increasing kernel rows from two in teosinte to more than eight in maize. John Doebley mapped a QTL underlying kernel row number domestication on chr2, and reported that Zfl2 might be important for this QTL (Bomblies K, Doebley JF. Pleiotropic effects of the duplicate maize FLORICAULA/LEAFY genes zfl1 and zfl2 on traits under selection during maize domestication. Genetics. 2006 Jan;172(1):519-31.). Here, Chen et al. examined the genomes of domestic maize and wild teosinte accessions for evolutionary signals of selection. From these sequences, the authors cloned a WD40 protein that controls the kernel row number domestication from teosinte to maize and the grain increase from wild rice to modern rice, even though maize and rice experienced independent selection. Field tests show that knockout of KRN2 in maize or OsKRN2 in rice increased grain yield by ~10% and ~8%, respectively, suggesting potential applications of KRN2 and its orthologs for crop improvement. Their results also suggested that identifying genes under selection in one cereal provides valuable fodder for crop improvements. Lei Liu, 2022

Zm00001d002641 = KRN2

Chen, WK, et al. 2022. Science. 375:DOI: 10.1126/science.abg7985
   Convergent selection of a WD40 protein that enhances grain yield in maize and rice
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Gage, JL, et al. 2022. Proc Natl Acad Sci, USA. 119:e2112516119
   Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance

There is low correlation between the mRNA and protein abundance across genes. Many different steps in regulation could explain this low correlation, such as differential rates in transcription or translation of different alleles of a gene. While GWAS is effective at detecting common SNPs that affect protein abundance, these are often considered low effect SNPs. High effect SNPs are rare and difficult to detect in GWAS. Thus, Gage et al. explores and describes how an upstream open reading frame (uORF) can differentially affect protein abundance in reference to a gene's main open reading frame (mORF). Exploring diverse maize inbred lines showed heritable levels of protein abundance that were comparable to the heritability levels of metabolites and mRNA. Using the maize HapMap population database, it was found that rare alleles in the 5' untranslated region (5' UTR) had the strongest association with variable protein abundance as compared to rare alleles in the coding sequence, intron, and 3' UTR of genes. In genes that normally have a uORF, the presence of a rare allele in the uORF appeared to weaken the translational efficiency of the transcript, leading to an increase in protein abundance of the related mORF. The presence of rare alleles in the uORF is also associated with an enrichment of GWAS hits in the mORF, suggesting and adaptive advantages of the mORF and common allele. On the converse, novel uORFs pulled translation away from mORFs, resulting in reduced associated mORF protein abundance and no enrichment of GWAS hits. While ORFs were correlated with changes in protein abundance, they were not correlated with mRNA abundance, suggesting the abundance of proteins is being regulated at the translational level. In all, this work suggests that it is possible to predict protein abundance from sequence information, improving the disconnect between mRNA and protein abundance. Lander Geadelmann, 2022

Gage, JL, et al. 2022. Proc Natl Acad Sci, USA. 119:e2112516119
   Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance
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Keller, B, et al. 2022. Plant Physiol. 188:301-317
   Toward predicting photosynthetic efficiency and biomass gain in crop genotypes over a field season

Photosynthesis is the physiological basis of plant growth and crop yield. A large portion of yield comes from photosynthesis which depends on the light interception efficiency (εi) to photochemical energy (εe) which later translates to biomass (εc). As this process is highly dynamic, it acclimates within seconds to fluctuations in light intensity and balances absorbed energy into two additional pathways, non-photochemical quenching (NPQ, 70%) and chlorophyll fluorescence (ChlF, 0.5% to 3%). Consequently, biomass accumulation is highly dependent on the environmental conditions during the growth period and the plant's ability to adapt those conditions. An investigation into the dynamic response of photosynthesis to the fluctuating environment was conducted in 12 maize and 9 soybean genotypes to understand the fundamental relationship between energy uptake and biomass accumulation over the growing period. Fq'/Fm' derived under incident sunlight during was modeled based on genotypic interactions with different environmental variables the entire growing season. The full models explained 45% and 53% of the Fq'/Fm' variance in maize and soybean, respectively. The adjusted Fq'/Fm' means and the ResponseG:PPFR of each genotype in each experiment were extracted and correlated with biomass production in all seven experiments (up to r = 0.68). Also, ETR could be precisely calculated over full seasons with r = 0.67 but the resulting biomass prediction was not accurate. In summary, the authors of this study integrated photosynthetic responses to environmental stresses over the growing season to estimate biomass production and identify energy-efficient genotypes. In the future, this could be used to improve crop growth models and to estimate the productivity of breeding lines or entire ecosystems at any point in time. Anuradha Singh, 2022

Keller, B, et al. 2022. Plant Physiol. 188:301-317
   Toward predicting photosynthetic efficiency and biomass gain in crop genotypes over a field season
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Cao, SA, et al. 2022. Genome Biology. 23:53
   Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize

In this paper the authors investigated trans-acting epialleles in reciprocal crosses of B73 and Mo17 followed by backcrossing to the pollen donor for 6 generations and selfing for three generations. They selected two lines with greater than 99% homozygosity with their recurrent parent for use in further analysis. They evaluated differential methylation in the CHH context, and found there were parent-of-origin effects. Through their investigation of methylation differences between generations, and the recurrent parent they found transgenerational inheritance of differentially methylated regions (tgDMRs), some of which overlapped structural variants and were found to be in places of low chromatin accessibility. Additionally they found high levels of 24nt siRNAs in the 5' regions of genes containing DMRs in that region. Overall their results suggest that paramutation is more common than we realize. Kaitlin Higgins, 2022

Cao, SA, et al. 2022. Genome Biology. 23:53
   Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize
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Sun, GL, et al. 2022. Plant Cell. 0:doi: 10.1093/plcell/koac047
   The maize single-nucleus transcriptome comprehensively describes signaling networks governing movement and development of grass stomata

Grass stomata is a fascinating model system to study the development and conductance of stomata. Their fast response to the environmental cues is due to the presence of subsidiary cells, flanking the guard cells. In this study, Sun et al. used the single nucleus RNA-seq to identify differentially expressed and cell-type specific genes during stomatal development and functionally important for rapid stomatal conductance. They have isolated nuclei from 5 cell types (pavement cells, guard cells, subsidiary cells, mesophyll cells, and bundle sheath-related cells) of maize leaf peels. In addition to several previously known genes expressed in a specific tissue type and developmental stages, they have found some new candidate genes and expressed them with fluorescent proteins to further confirm the localization pattern. Among these candidate genes, authors also tested the drought response of zmmpk12 mutant. Altogether, this study provides the single nucleus RNA-seq dataset for maize stomatal development and movement study in future. Arif Ashraf, 2022

Sun, GL, et al. 2022. Plant Cell. 0:doi: 10.1093/plcell/koac047
   The maize single-nucleus transcriptome comprehensively describes signaling networks governing movement and development of grass stomata
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Linnen, C; Brandvain , Y; Unckless , R. 2022. Evolution. 0: DOI: 10.1111/evo.14444
   Theme: Recent work in speciation research by women authors

This article was selected in commemoration of Women's History Month. It provides a list and some overall characteristics of 26 key papers on speciation published by women in the journal Evolution over the last three decades. I found this perspective paper interesting because it gives an outlook on the contributions of women that have been hidden behind more famous men while describing some of the barriers women have faced in this field that overshadow their contributions. The paper reminds us to be keen in supporting the contribution and influence of women in various fields and to be watchful of the existing barriers that overshadows women's efforts and contributions. Andrew Egesa, 2022

Linnen, C; Brandvain , Y; Unckless , R. 2022. Evolution. 0: DOI: 10.1111/evo.14444
   Theme: Recent work in speciation research by women authors
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Yang, T, et al. 2022. Plant Cell. 0:doi: 10.1093/plcell/koac044
   ABA-induced phosphorylation of basic leucine zipper 29, abscisic acid insensitive 19 and opaque2 by SnRK2.2 enhances gene transactivation for endosperm filling in maize

O2 is a master regulator of grain filling in maize, but its regulation at transcriptional and post-transcriptional levels is still not fully understood. In this study, the authors found that ZmbZIP29 binds the ABRE in the O2 promoter and transactivates O2 expression. ZmbZIP29 is highly expressed in seeds at a very early stage (2-8 days after pollination). Loss-of-function of ZmbZIP29 leads to reduced O2 expression and diminished grain filling. The authors further found that ZmbZIP29 interact with ZmABI19, and the two transcription factors act synergistically to promote O2 expression. Consistent with this, the bzip29/abi19 double mutant displays much more severe defects in grain filling compared with single mutants, while over-expression of ZmABI19 or ZmbZIP29 significantly enhanced O2 expression and maize grain yield. The authors also identified SnRK2.2 as an pivotal regulator of ZmABI9, ZmbZIP29 and O2: SnRK2.2 phosphorylates all three transcription factors and increase their transactivation activity. Hai Wang, 2022

Cereal grains accumulate large amounts of proteins and starch and are a major source of dietary calories for humans and animals. In maize, most of the storage compounds are synthesized during the grain-filling period of kernel development. Therefore, the initiation of endosperm filling is a critical phase of seed development during which endosperm-filling regulatory TFs are activated, leading to rapid synthesis and accumulation of starch and zein proteins in the maize endosperm. It is already known that Opaque2 (O2) functions as a central regulator of the synthesis of starch and storage proteins, and transcriptionally regulated by a hub coordinator of seed development and grain filling, ABSCISIC ACID INSENSITIVE 19 (ZmABI19), in maize. However, the overall picture of the regulatory networks involved in seed development is still unclear. In this study, by analyzing the high-resolution RNA-seq data and yeast one-hybrid (Y1H) assay results, Yang et al. found that ZmbZIP29 which is also an ABA-inducible TF can directly regulate O2 expression in endosperm via interacting with ZmABI19. Moreover, they demonstrated that ZmbZIP29 and ZmABI19 mutations cumulatively influence seed development and storage protein synthesis by performing overexpression and knockdown experiments. Finally, by analyzing Y2H assay and liquid chromatography tandem-mass spectrometry results they discovered that SnRK2.2, strongly induced by ABA, can phosphorylate the residues threonine(T) 57 in ZmABI19, T75 in ZmbZIP29, and T387 in O2. Overall, their results show us a much clearer and more complete regulatory network in which ZmbZIP29, ZmABI19, and O2 were phosphorylated by ABA-induced SNRK2.2, leading to the increased O2 expression and in turn the expression of down-stream genes for endosperm filling in maize. Beibei Liu, 2022

Yang, T, et al. 2022. Plant Cell. 0:doi: 10.1093/plcell/koac044
   ABA-induced phosphorylation of basic leucine zipper 29, abscisic acid insensitive 19 and opaque2 by SnRK2.2 enhances gene transactivation for endosperm filling in maize
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Yu, Y; Zhang, H; Long, Y; Shu, Y; Zhai, J. 2022. Plant Biotechnol J. 0: https://doi.org/10.1111/pbi.13798
   Plant Public RNA-seq Database: a comprehensive online database for expression analysis of ~45,000 plant public RNA-Seq libraries

There are many public gene expression databases for maize, such as MaizeGDB and qTeller. Yu and colleagues reported another alternate database, named PPRD, short for Plant Public RNA-seq Database (http://ipf.sustech.edu.cn/pub/plantrna/). PPRD consists of a large number of RNA-seq libraries of maize (19,664), rice(11,726), soybean (4085), wheat (5816) and cotton (3483) from Gene Expression Omnibus (GEO), Sequence Read Archive (SRA), European Nucleotide Archive (ENA) and DNA Data Bank of Japan(DDBJ) databases These datasets come from different mutants, tissues, developmental stages and abiotic or biotic stresses. They processed the data of each species with a unified pipeline and the most up-to-date reference genomes to reduce the quantification biases derived from differing bioinformatic processes. It is a very useful database to check the expression of your genes, and returns the multiple forms of results in tables and diagrams, showing the expression levels in various tissues, developmental stages, abiotic stresses, biotic stresses, as well as the differential expression in different mutants and treatments. Lei Liu, 2022

http://ipf.sustech.edu.cn/pub/plantrna/

Yu, Y; Zhang, H; Long, Y; Shu, Y; Zhai, J. 2022. Plant Biotechnol J. 0: https://doi.org/10.1111/pbi.13798
   Plant Public RNA-seq Database: a comprehensive online database for expression analysis of ~45,000 plant public RNA-Seq libraries
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Nelms, B; Walbot, V. 2022. Science. 375:424-429
   Gametophyte genome activation occurs at pollen mitosis I in maize

During reproductive development, the haploid genome and gene expression patterns must replace the diploid genome, but when this switch occurs and how these dynamics play out are unknown. Maize pollen has distinct stages of development. The pollen mother cell is the pollen precursor and undergoes meiosis, resulting in the tetrad stage with four potential gametes to continue through pollen development. Each gamete grows into the unicellular stage, then develops through a bicellular and tricellular stage. Through allele-specific RNA-seq of F1 hybrid pollen, Nelms and Walbot reveal changes in genes expression are not uniform over the course of pollen development. There is a rapid change in transcription associated with prophase I, a steady transcriptional state from metaphase I through the early unicellular stage, and a second rapid change in transcription during pollen mitosis from unicellular to bicellular microspores. The presence of biallelic transcripts were detecting into the unicellular stage, and it was not until the bicellular stage that genes showed rapid and widespread expression of monoallelic expression. The suggests that storage of mRNA could play a role in pollen development. Due to the design of the experiment, transcription rates of genes can be estimate using haploid specific transcripts. Examination of this time series data supports the conclusion that developing cells are provisioned with diploid transcripts, and that increased transcriptional activity at the bicellular stage drives the haploid takeover of gene expression. Once in the haploid state and presumably lacking provisioned transcripts, Nelms and Walbot detect almost one-third of genes are under purifying-selection. This differs from early pollen development, which more closely resembles the diploid sporophyte stage. Thus, this work furthers our understanding of gametophyte specific expression and provides a framework for future experiments on maize pollen. Lander Geadelmann, 2022

Nelms, B; Walbot, V. 2022. Science. 375:424-429
   Gametophyte genome activation occurs at pollen mitosis I in maize
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Xu, Q, et al. 2022. Genome Biology. 23:77
   DNA demethylation affects imprinted gene expression in maize endosperm

DNA demethylation is a biological process universally present in many species, but its regulation and function is still obscure in maize. The maize genome encodes 4 DNA demethylases (ZmROS1a-d). Among them, ZmROS1a and ZmROS1b are most highly expressed, expecially in embryo and endosperm. The authors obtained loss-of-function mutants of both genes, and also their double mutant. Whole-genome bisulfite sequencing using embryo and endosperm in WT and the mutant genotypes superisingly revealed that the global DNA methylation levels are quite similar between WT and the single and double mutants. Nevertheless, the authors do observed increased DNA methylation levels around genes and some TEs in the mutants, accompanied by altered (mostly down-regulated) gene expression. Interestingly, In F1 hybrid with the mutant as female parental line and the WT as male parental line, the authors observed significant changes in the imprinted expression of both MEGs and PEGs. This phenomenon was absent in F1 hybrid with the mutant as male parental line and the WT as female parental line. Thus removal of DNA methylation of the maternal allele is required for the proper expression of imprinted genes. The authors also proved that the hyper-methylation in the double mutant is associated with reduced binding of TFs to their targets. Taken together, this study revealed a pivotal role of active removal of DNA methylation in TF-DNA interaction and proper gene expression in maize endosperm. Hai Wang, 2022

Zm00001d038302 = ZmROS1a = ros1 - repressor of silencing1 in MGDB

Zm00001d053251 = ZmROS1b = mdr1 - maternal derepression of R1 in MGDB

Zm00001d016521 = ZmROS1c = dng105 - DNA glycosylase105 in MGDB

Zm00001d016516 = ZmROS1d = dng102 - DNA glycosylase102 in MGDB

Xu, Q, et al. 2022. Genome Biology. 23:77
   DNA demethylation affects imprinted gene expression in maize endosperm
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Minow, MAA; Lukens, LN; Rossi, V; Colasanti, JJ. 2021. Genome. 0:doi: 10.1139/gen-2021-0040
   Patterns of stability and change in the maize genome: a case study of small RNA transcriptomes in two recombinant inbred lines and their progenitors

In this paper, the author and collaborators explored the differences in sRNA expression between recombinant inbred lines (RILs) and their inbred parents. Using previously published mRNA data from V1 stage roots, and the B73v4 genome assembly, they identified polymorphisms between the inbred parents and used unique polymorphisms to identify which region of the RIL was inherited from each parent. They then mapped the sRNA reads and used pairwise comparisons to determine differential expression. Interestingly, novel sRNA transcripts were rare (<1% of all sRNA clusters). Instead what the authors found was that the region an sRNA cluster mapped to often shared expression levels with the parent the region had been inherited from, but about 22% of all expression differences did not share similarity with the haplotype parent, and instead had similar expression to the homologous region in the other parent though it was often downregulated comparatively. Further, they found that the RILs tended to be more similar to each other than their inbred parents in regions where expression was similar to the non-haplotype parent. Overall their work suggests that sRNA expression is largely inherited from the haplotype parent, and indicates that there may be trans acting elements influencing similarity between RILs. Kaitlin Higgins, 2022

Minow, MAA; Lukens, LN; Rossi, V; Colasanti, JJ. 2021. Genome. 0:doi: 10.1139/gen-2021-0040
   Patterns of stability and change in the maize genome: a case study of small RNA transcriptomes in two recombinant inbred lines and their progenitors
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Laureyns, R, et al. 2021. Plant Physiol. 0:doi:10.1093/plphys/kiab533
   An in situ sequencing approach maps PLASTOCHRON1 at the boundary between indeterminate and determinate cells

Spatial transcriptomics/in situ sequencing (ISS) enables researchers to sequence individual cells while maintaining significant physiological context. Laureyns et al. have worked to optimize ISS technology for the maize shoot apical meristem (SAM). Through their validation, they describe potential ways ISS research can be compounded in plants, such as the need for consistent aligning of sections on specific plant organs and the influence of distinct cell layers on gene expression. A panel of 90 genes was used to verify observed expression patterns matched previous in situ expression pattern. 63 out of 90 genes were successfully detected. Of the genes that were not detected, the failure to amplify target genes was attributed to probe design or other technical artifact. One such potential artifact, optical crowding, where the simultaneous sequencing of multiple genes inhibits each other amplification and sequencing, was detected and described. In a final validation of the ISS technology for the SAM, expression profiles of genes known to mark specific tissues in the meristem region were observed, confirming the accuracy of ISS. After validation, ISS was used to understand the expression pattern of PLASTOCHRON1 (PLA1). PLA1 plays a role in cell division and is believed to interact with genes that are expressed in indeterminate cells. The expression pattern, however, remains unknown. ISS reveals PLA1 is expressed at the base of leaf primordia and overlaps the boundary between indeterminate and determinate cells, supporting a role in leaf growth and plastochron regulation. Expression at indeterminate/determinate boundaries was also observed in ear spikelets. The PLA1 expression pattern overlaps with other genes known to establish and regulate organ boundaries, further supporting PLA1's role in cell differentiation. PLA1 is not expressed in areas of the meristem with high levels of auxin or cytokinin, suggesting that its regulatory activity functions downstream of these two hormones. This work greatly contributes to the technological toolbox of maize research, providing and intermediary between high resolution single-cell sequencing and the preservation of expression patterns in physiological context. Lander Geadelmann, 2022

Laureyns, R, et al. 2021. Plant Physiol. 0:doi:10.1093/plphys/kiab533
   An in situ sequencing approach maps PLASTOCHRON1 at the boundary between indeterminate and determinate cells
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Lunsford, L; Arthur , M; Porter, CM. 2021. 0:10.5304/jafscd.2021.104.008
   African and Native American foodways and resilience: From 1619 to COVID-19

Invasion, enslavement, and supremacy have in many ways built the current food systems of the Americas and the Caribbean. while at the same time disrupting existing systems that built. They have and still do cut deeply into the lives of African and Native American communities and have disrupted well-established food systems for new ones aiming to make these same communities reliant on limited resources. Important stories remain untold of the resiliency of these communities and the ways their customs for producing, preparing, using, and exchanging goods and services for and with food (their foodways) have adapted. The authors compiled literature, interviews, and their own experience to create a history, a re-story, of the foodways of African and Native Americans divided into six eras spanning from 1619 through 2020. I read with a focus on African American communities. I found it compelling to learn about major historical events, cultural trends, and current health disparities through the lens of food. I enjoyed learning about relationships African American communities have had with the land and their food over the last 400 years. The paper helped me appreciate the agency that comes with having control of what you eat, and it presents ideas of how we can restore and promote it. Tessa Durham Brooks, 2022

Lunsford, L; Arthur , M; Porter, CM. 2021. 0:10.5304/jafscd.2021.104.008
   African and Native American foodways and resilience: From 1619 to COVID-19
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Eckelbarger, M, et al. 2021. Trends Plant Sci. 0:10.1016/j.tplants.2021.07.021
   Recognizing pioneering Black plant scientists in our schools and society

Knowledge, inventions, and innovations in different fields, including plant science, drive better life and primarily benefit from individuals who dedicate their time and energy to their pursuit. However, historically underprivileged groups such as Black and Indigenous People of Color (BIPOC) face challenges obtaining skills and opportunities to create knowledge, inventions, and innovations. Many BIPOC who overcome these challenges to pursue science have awarded us discoveries and knowledge that have significantly improved our lives today, underscoring the critical importance of diversity and inclusion in science. As a way of celebrating and creating awareness of the contribution of BIPOC in plant science, Eckelbarger et al. (2021) organized an exhibition at Historically Black Colleges and Universities, Hispanic Serving Institutes and Primarily Undergraduate Institutions, where they highlighted the life and achievements of some pioneer BIPOC plant scientist and used their stories to break race barriers to participation in science. In this paper, Eckelbarger et al. (2021) present a pre-exhibit summary highlighting life and achievements of four BIPOC; Edmond Albius (a prodigy of pollination), Marie Clack Taylor (Educationist), George Washington Carver (Chemist and Agronomist) and Percy Lavon Julian (Botanical chemist). Their profound achievements and work made the world we live in better. This is a good read; it educates us on the contributions of BIPOC in Science and informs us on how we can celebrate BIPOC scientists and use such initiatives to promote the involvement of BIPOC in Science. Andrew Egesa, 2022

Eckelbarger, M, et al. 2021. Trends Plant Sci. 0:10.1016/j.tplants.2021.07.021
   Recognizing pioneering Black plant scientists in our schools and society
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Zhao, BB, et al. 2022. Plant Biotechnol J. 0:doi: 10.1111/pbi.13787
   Overexpression of ZmSPL12 confers enhanced lodging resistance through transcriptional regulation of D1 in maize

ZmSPL12 = Zm00001d015410

One big challenge for high-density-tolerant crop breeding is increasing lodging resistance. Semidwarf plant architecture can improve lodging resistance and is often used for dense planting varieties. Semidwarf genes, such as sd1 and Rht1 involved in GA signaling pathway, were applied in the first "green revolution" in rice and wheat. The maize d1 gene can efficiently reduce plant stature but have severe negative yield traits. In this paper, the authors found that ZmSPL12 specifically binds to the promoter of D1 and represses the transcription of D1. Zmspl12 knock-out alleles increased plant height, whereas overexpressing ZmSPL12 decreased plant height. ZmSPL12-OE could enhance high-density maize yields and logging resistance. Introgressing ZmSPL12-OE into modern maize inbreds can confer logging resistance. Therefore, ZmSPL12 is suggested as an important gene for developing high-density-tolerant crop varieties. Lei Liu, 2022

Zhao, BB, et al. 2022. Plant Biotechnol J. 0:doi: 10.1111/pbi.13787
   Overexpression of ZmSPL12 confers enhanced lodging resistance through transcriptional regulation of D1 in maize
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Liu, P, et al. 2022. BMC Genomics. 23:50
   Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress

Other differentially expressed genes: Zm00001d001353 Zm00001d016139 Zm00001d044281 Zm00001d044281 Zm00001d040038 Zm00001d046587

Maize (Zea mays L.) is a worldwide cultivated crop and sensitive to salt stress, particularly at the seedling stage. Although more and more evidence supported that lncRNAs play significant roles in stress response, only a few lncRNAs have been reported to involve salinity stress at a whole transcriptome level. Therefore, to reveal the salt stress-responsive lncRNAs and the mechanism underlying salt tolerance, Liu et al. analyzed the whole transcriptome sequencing data of two maize inbred lines BML1234 (salt-sensitive) and L2010-3 (salt-tolerance) at different salt treatment stages and normal conditions. They identified 598 and 114 differentially expressed lncRNAs (DELs) which were specifically responsive to salt stress in BML1234 and L2010-3, respectively. To predict the targets of these lncDNAs, 5,672 and 1,753 differentially expressed mRNAs (DEMs) were identified in BML1234 and L2010-3. In total, 168 lncRNA-mRNA pairs including 123 trans- and 45 cis- pairs were detected and speculated to be involved in salt tolerance in maize seedlings. Among these target transcripts, 11 belonged to 7 transcription factor (TF) families including bHLH, C2H2, Hap3/NF-YB, HAS, MYB, WD40, and WRKY. Furthermore, salt stress-responsive transcripts were classified into 28 modules by weighted gene co-expression network analysis. Finally, the salt stress-related regulatory pathway, which was mediated by the hub lncRNA MSTRG.8888.1, participated by the bHLH TF, and its downstream target transcripts were constructed in maize seedlings. In summary, these results provide some insights into how lncRNAs were involved in the salt stress response by affecting the expression of protein-coding genes in maize. BeiBei Liu, 2022

Liu, P, et al. 2022. BMC Genomics. 23:50
   Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress
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Hostetler, AN, et al. 2022. Plant Cell Environ. 0:doi: 10.1111/pce.14289
   Multiple brace root phenotypes promote anchorage and limit root lodging in maize

Brace roots support maize plants for anchorage and help to avoid the lodging during adverse conditions. But the genetic circuit for lodging resistance is not known. In this study, Hostetler et al. tested 52 maize inbred lines for two years to find out the genetic parameters involved in this process. Their finding suggests that variation in genotype contributes to the plant architecture and as well as phenotype of brace root, which help to the anchorage. Several plant architecture parameters such as plant height, stalk width, and root angle were highlighted as the best predictor for plant lodging susceptibility. Based on their genotype wide observation, they have identified 16 root lodging resistant genotypes (B104, CML228, 6M502, CML277, Hp301, PHR58, CML373, L163, Kil1, Ms71, A632, Mo17, PHK46, PHHB4, Ki3, and CML322). This study opened the door to find out the genetic regulator for lodging resistance mechanisms in the near future. Arif Ashraf, 2022

Hostetler, AN, et al. 2022. Plant Cell Environ. 0:doi: 10.1111/pce.14289
   Multiple brace root phenotypes promote anchorage and limit root lodging in maize
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Li, Y, et al. 2021. J Integr Plant Biol. 0:doi: 10.1111/jipb.13198
   ZmGRAS11, transactivated by Opaque2, positively regulates kernel size in maize

Li et al. tested 137 elite inbred lines of maize for their kernel length, thickness, and width. To find the causative gene for regulating kernel size, authors used single nucleotide polymorphisms (SNPs) and identified a candidate region which encodes ZmGRAS11. Furthermore, authors have found that ZmGRAS11 expresses during the kernel development and expression QTL (eQTLs) data suggest that Opaque2 (O2) is regulating the expression of ZmGRAS11. Electrophoretic mobility shift assay (EMSA) and dual-luciferase transactivation assay confirmed that O2 directly binds the promoter region of ZmGRAS11. To identify the role of ZmGRAS11 expression for kernel development, authors have used mutants (zmgras11-Dsg1 and zmgras11-Dsg2) and overexpression line of ZmGRAS11 and demonstrated the opposite effect for kernel length, width, and weight. This study highlighted the molecular role of ZmGRAS11 for grain yield and can be useful as a molecular breeding in future. Arif Ashraf, 2022

Gene: ZmGRAS11 = GRMZM2G023872

Li, Y, et al. 2021. J Integr Plant Biol. 0:doi: 10.1111/jipb.13198
   ZmGRAS11, transactivated by Opaque2, positively regulates kernel size in maize
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Wu, J, et al. 2022. Nature Biotechnology. 40:10.1038/s41587-021-01176-z
   Virtual meetings promise to eliminate geographical and administrative barriers and increase accessibility, diversity and inclusivity

Following the outbreak of Covid-19 pandemic two years ago, scientific societies, research institutions and their affiliates promptly shifted to online virtual platforms, especially zoom, Google meet among others as the most viable ways of continuing with conferences, workshops, summits, and trainings. This was critical for advancing science and knowledge amid the worldwide health crisis. However, other benefits that came with these changes are obscured by diverse challenges associated with mainstream virtual platforms, spanning, technical, technological, economical aspects and fatigue from these unpopular ways of doing business. In this paper, Wu et al, 2021 discusses actual shifts in participation in scientific academic conferences, especially the beneficial increase in diversity of attendance from underrepresented groups such as women and people from developing/poor economy countries for global conferences. Authors discuss these observations with respect to a lift to barriers such as high cost of registration for in-person meetings, travel barriers, administrative challenges, and increased flexibility among others. This paper is interesting because, it uses actual conference attendance data in confirming the shifts in attendance as influenced by adoption of virtual platforms, indicating possible conference attendance barriers among underrepresented groups that may be of interest to scientific communities. Andrew Egesa, 2022

Wu, J, et al. 2022. Nature Biotechnology. 40:10.1038/s41587-021-01176-z
   Virtual meetings promise to eliminate geographical and administrative barriers and increase accessibility, diversity and inclusivity
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Anderson, SN; Zhou, P; Higgins, KM; Brandvain, Y; Springer, NM. 2021. PLoS Genetics. 17:e1009491
   Widespread imprinting of transposable elements and variable genes in the maize endosperm

In this paper, the authors develop a new method (RER) for identifying imprinted genes that display presence-absence variation(PAV) within maize. Imprinted genes are those that are expressed dependent on which parental lineage an allele is inherited from, and are primarily expressed in endosperm. The RER method relies on the expression ratios of two different genomes, with the expected expression of biparentally expressed genes in endosperm being ~.66. This enables us to determine imprinted status of PAV genes and transposable elements by comparing expression ratios in reciprocal crosses, the expectation being a lower or absent expression in one direction of the reciprocal cross. Indeed, the authors identified many imprinted genes displaying PAV, the majority of which were maternally expressed genes and transposable elements. This new method will be an excellent resource for identifying and exploring imprinted genes so that we can investigate their role in maize endosperm more thoroughly. Kaitlin Higgins, 2022

Anderson, SN; Zhou, P; Higgins, KM; Brandvain, Y; Springer, NM. 2021. PLoS Genetics. 17:e1009491
   Widespread imprinting of transposable elements and variable genes in the maize endosperm
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Wang, K, et al. 2022. Nature Plants. 0:https://doi.org/10.1038/s41477-021-01085-8
   The gene TaWOX5 overcomes genotype dependency in wheat genetic transformation

Genetic transformation technology is critical for genetic and molecular biology research, especially for the rapid application of genome editing. However, the transformation of cereal crops is not easy, such as wheat, maize, barley. There are some alteration methods to employ some "enhancers" in cereal crops published in recent years, for example, using somatic embryogenesis receptor kinase (SERK), LEAFY COTYLEDON (LEC1), LEAFY COTYLEDON2 (LEC2), NiR, BABY BOOM (BBM)-WUSCHEL (WUS) and GRF4-GIF1. In this paper, the authors reported that overexpression of the wheat gene TaWOX5 dramatically improves the transformation frequency of wheat and five other cereal species in various genotypes, including maize. Based on the results in the paper, the overexpression of TaWOX5 could lead to a 23.2 +/- 4.0% transformation rate in B73, which looks very exciting. Lei Lui 2022

Wang, K, et al. 2022. Nature Plants. 0:https://doi.org/10.1038/s41477-021-01085-8
   The gene TaWOX5 overcomes genotype dependency in wheat genetic transformation
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Klein, H, et al. 2022. Proc Natl Acad Sci, USA. 119:e2115871119
   Recruitment of an ancient branching program to suppress carpel development in maize flowers

Maize male and female flowers follow similar steps of development and deviate in patterns of floral meristem suppression/abortion to give rise to the tassel and ear, respectfully. In tassels, carpel formation is suppressed, preventing silk formation, leaving only stamen at a fully formed flower. The gene GRASSY TILLERS1 (GT1) has been shown to have a weak carpel suppression phenotype. Klein et al. sought to find additional regulators of carpel suppression though an enhancer screen of gt1 mutants. An initial EMS enhancer screen led to the identification of two new alleles for RAMOSA3 (RA3). The gt1; ra3 double mutant exhibits derepressed carpel formation and the emergence of silks in the tassel. Carpel depression also results in additional silk formation in the ear. The indeterminate branching phenotypes in both the tassel and ear of ra3 mutants is reduced in the gt1; ra3 double mutant. Both GT1 and RA3 colocalize in the nucleus of carpel primordia, suggestion that these two proteins work together in a cell autonomous fashion. Differential expression analysis before and during carpel suppression showed downregulation of genes predicted to mediate programmed cell death in the double mutant. Almost one-third of these differentially expressed genes were also present in differential expression datasets comparing gt1 mutant and wild-type tiller gene expression. Past research has shown that RA3 and GT1 bind to TEOSINTE BRANHCED1 (TB1), a known regulator of tillering. The gt1; ra3 double mutant has more and longer tillers, and more ears, than gt1 single mutants. This work reveals a novel interaction between two well characterized genes and describes their pleiotropic functions during maize development. Lander Geadelmann, 2022

gt1 GRMZM2G005624 ra3 GRMZM2G014729

Raw sequencing data are available at the National Center for Biotechnology Information BioProjects (RNA-seq: PRJNA657042; ra3-rzl4 BSA-seq: PRJNA656888); all data underlying the figures are available either in SI Appendix or in Datasets S1 and S2.

Klein, H, et al. 2022. Proc Natl Acad Sci, USA. 119:e2115871119
   Recruitment of an ancient branching program to suppress carpel development in maize flowers
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Cheng, CY, et al. 2021. Nature communications. 12:5627
   Evolutionarily informed machine learning enhances the power of predictive gene-to-phenotype relationships

Cheng et al. used evolutionarily conserved gene expression datasets within and across species to create a machine learning model that predicts nitrogen use efficiency (NUE) genes in maize and Arabidopsis. They also applied this model to previously published transcriptome/phenotype datasets in rice and mouse. The authors validate the model by functionally characterizing seven candidate transcription factors in maize and Arabidopsis. The machine learning pipeline integrates phenotype, transcriptome data, genetic variation, and environmental responses to; 1. preselect subsets of transcripts based on conserved transcriptome data within and across species, 2. Use this conserved data as a biologically based way to improve the machine learning model, and 3. Rapidly validate the function of "important gene features". This study is significant because it shows that using an evolutionarily conserved dataset for machine learning allows a biologically principled method to improve the predictive power of genotype to phenotype. The authors emphasize the power of their method and state that this work could be applied to biological, agricultural, and medical trials to uncover genes involved in complex phenotypes. Brianna Griffin, 2021

"The curse of dimensionality", i.e. too many predictors compared with the number of observations, causes overfitting in machine learning. This problem is especially severe when predicting phenotypes using molecular markers as predictors. To reduce the number of predictors, an alternative approach is to use molecular phenotypes (such as gene expression levels) as predictors. However, the number of genes is still often far more than the number of observations. In this study, the authors used gene expression levels to predict nitrogen use efficiency (NUE). To reduce the number of genes, inter- or intra-species conserved nitrogen-responsive genes where chosen as predictors. They showed that evolutionarily informed feature selection effectively reduced the dimensionality of predictors, and ultimately improved the predictive accuracies in some genetic backgrounds, although this model cannot predict which genetic background would perform better in NUE (Fig. 5, Step 3). The authors further functionally validated several candidate transcription factors with predictive power for NUE, demonstrating the power of this approach to uncover novel genes controlling NUE. Hai Wang, 2022

Cheng, CY, et al. 2021. Nature communications. 12:5627
   Evolutionarily informed machine learning enhances the power of predictive gene-to-phenotype relationships
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Zhang, YR, et al. 2022. BMC Genomics. 23:4
   Transcriptomic analysis of the maize inbred line Chang7-2 and a large-grain mutant tc19

Grain size is an important trait of grain weight which is the primary affecting factor of crop yield. In the case of maize grain development, most studies focused on small-grain mutants, only a few studies used large-grain mutants. To investigate the developmental mechanisms of grain size, Zhang et al. analyzed Chang 7-2, one of the maize elite inbred lines in China, and tc19, a large-grain mutant, at the morphological and transcriptome level of five stages corresponding to days after pollination (DAP). At the morphological level, their data demonstrated that the length, width, thickness, and 100-kernel weight of the mature seeds of tc19 were significantly greater than those in Chang7-2. More importantly, their data showed that grain width was the main contributor to the difference in grain size between Chang7-2 and tc19, and the stage between 14 to 28 DAP is an important period for grain enlargement. At the transcriptome level, they found lots of differently expressed genes (DEGs) between Chang7-2 and tc19, and most of them were significantly enriched in the hormone signal transduction pathway. Although many plant hormones (abscisic acid (ABA), ethylene (ET), jasmonic acid (JA)) contribute to the increased grain, their data demonstrated that auxin and brassinolide contribute significantly to the enlarged size of the tc19 grains. Overall, their results provide some insights into how hormone-related genes might affect the grain size by investigating the large-grain mutant tc19. Beibei Lai, 2022

ARF3 (arftf26) (Zm00001d012731), IAA15 (iaa8) (Zm00001d039624), AO2 (ao4) (Zm00001d034388), DWF4 (drg10)(ZM00001d003349), XTH (xth4) (Zm00001d014617)

BioProject PRJNA724904 (NCBI). May not be public.

Zhang, YR, et al. 2022. BMC Genomics. 23:4
   Transcriptomic analysis of the maize inbred line Chang7-2 and a large-grain mutant tc19
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Stachl, C; Baranger, A. 2020. PLoS One. 15:e0233431
   Sense of belonging within the graduate community of a research-focused STEM department: Quantitative assessment using a visual narrative and item response theory

An individual's sense of belonging within a community directly contributes to their self-efficacy, persistence, and achievement within it. Fostering belonging is essential to building successful, inclusive STEM programs. In this paper, sense of belonging was measured among graduate students, postdoctoral researchers, and faculty members in the UC Berkeley Chemistry department. Their data showed that graduate students derive a high sense of belonging from the community they formed with each other, which occurred primarily through a required teaching assignment completed in the first semester. Conversely, the interactions of graduate students (and postdoctoral researchers) with faculty generally had a negative impact on their sense of belonging. Based on their analysis, some of this was because unlike teaching, research was not regularly discussed between labs or completed collaboratively. A related contributing factor was the lack of opportunity to interact with faculty at a personal level. Another interesting outcome was that several indicators of imposter phenomenon were widely observed, occurring in over two thirds of respondents. The department reviewed these data together and as a result is offering culturally-sensitive mentorship training, hosting social events, and running a seminar series in which speakers talk about their scientific hurdles and failures. I found this to be a very exciting study that provides a framework for any program to use in identifying ways to make their own programs more inclusive. Tessa Durham Brooks, 2022

Stachl, C; Baranger, A. 2020. PLoS One. 15:e0233431
   Sense of belonging within the graduate community of a research-focused STEM department: Quantitative assessment using a visual narrative and item response theory
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Ortiz-Ramirez, C, et al. 2021. Science. 374:1247-1252
   Ground tissue circuitry regulates organ complexity in maize and Setaria

Ground tissue in the plant root is divided into two cell types: endodermis and cortex. But the number of cortex cell layers varies across the plant species. Ortiz-Ramirez et al. experimentally explained how multiple cortex cell layers formed in maize compared to a single layer in Arabidopsis thaliana. They used differentially penetrable labeling dyes, Syto 40 blue and Syto 81 green, to sort cells for scRNA-seq (single cell RNA sequencing) and identified 4 different cortex subtypes from the cluster analysis. Interestingly, they observed that SHORT-ROOT protein (SHR) is expressed in the endodermis in maize compared to the stele cells in Arabidopsis. As SHR moves from stele to endodermis in Arabidopsis, authors tested the mobility of SHR in maize. Translational fusion of SHR protein moves from endodermis to 8 layers of cortex. The hypermobility of SHR protein in multiple cortex cell layer development has been examined using double mutant Zmshr2/2-hand showed that cortical cell layers are reduced. Altogether, this study suggests that SHR expression in the endodermis cell layer and hypermobility of the protein to the cortex regulates the development of multiple layers of cortex in maize. Arif Ashraf, 2022

Zm00001d029607 = ZmSHR1 (gras58), Zm00001d021973 = ZmSHR2 (gras19), Zm00001d006721 = ZmSHR2-h (gras85), Zm00001d052380 = ZmSCR1 (scro1), Zm00001d005029 = ZmSCR2 (gras37), Zm00001d042821 = ZmWOX5B (wox5b)

Ortiz-Ramirez, C, et al. 2021. Science. 374:1247-1252
   Ground tissue circuitry regulates organ complexity in maize and Setaria
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Muyle, A, et al. 2020. Molecular Plant. 0:doi: 10.1016/j.molp.2020.11.003
   Gene capture by transposable elements leads to epigenetic conflict in maize

Transposable elements often capture fragments of genes, but it is unclear if this process affects in trans the function of the donor genes. We show that capture triggers an intragenomic conflict. The outcome of this conflict varies according to the functional importance of the gene and may range from no change in expression levels to loss of function and pseudogenization.

Muyle et. al., explore the epigenetic consequences of fragments of gene captured by transposable elements (TEs) in maize. As they say in the abstract, "When the host silences these TEs, siRNAs homologous to the captured regions may also target the genes". For genes which have TE captured fragments somewhere else in the genome, they explore siRNA accumulation, synteny with sorghum, and methylation levels at the genes. They find syntelogs with captured fragments show higher methylation and accumulate more siRNAs than their non-captured counterparts and a particularly high level of 24nt siRNA accumulation at the captured region suggesting a strong role for RdDM activity in the epigenetic cross talk of TEs capturing genes. They conclude the paper by pointing out that we still need to explore how consistent these results are across TE types since they only explored three (Helitrons, Pack-MULEs, and SirevirusLTR retrotransposons), as well as investigating how pervasive this effect is across species with higher methylation and TE loads. The authors suggest that if research can discern whether capture by TEs is mechanistically linked with gene translocation across lines it could be a main route to pseudogenization. Kaitlin Higgins, 2022

Muyle, A, et al. 2020. Molecular Plant. 0:doi: 10.1016/j.molp.2020.11.003
   Gene capture by transposable elements leads to epigenetic conflict in maize
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Luo, Y, et al. 2021. New Phytol. 0:doi: 10.1111/nph.17882
   Genetic variation in YIGE1 contributes to ear length and grain yield in maize

other genes that interact with yige1: Zm00001d028840 Zm00001d013356 Zm00001d037906

Ear length (EL) is a key component of grain yield in maize, but very few genes controlling EL have been cloned. In this study, Luo et al. mapped an EL QTL by GWAS in an association panel of 540 inbred lines. Fine mapping of this QTL identified the causal gene which they named YIGE1 (GRMZM2G008490, based on v2 annotation). Overexpression of YIGE1 increased female inflorescence meristem (IM) size, ear length, and kernel numbers per row, while loss-of-function of YIGE1 leads to decreased IM size and EL, confirming that YIGE1 is a positive regulator of EL. The detailed molecular mechanism of YIGE1 is still unknown, although some evidence shows that it may be involved in sugar and auxin signal pathways. The closest homolog of YIGE1 that has been functionally characterized is the HCF243 gene in Arabidopsis. However, YIGE1 and HCF243 have different subcellular localizations and thus most probably different molecular functions. The authors further tried to pinpoint the causal variant on YIGE1 in the association panel. They found that the SNP located in the regulatory region of YIGE1 had strong effect on its promoter strength. The cloning of YIGE1 and the identification of the favorable allele will facilitate maize genetic improvement. Hai Wang, 2022

This paper reports a new gene yige1, and connects it to GRMZM2G008490 in B73 Ref_V2, and Zm00001d028915 in B73 v4. Sequence is here: https://www.ncbi.nlm.nih.gov/nuccore/OK321185

yige1 is the causal gene for qEL1 and positively regulates the trait EL (Ear Length).

Ear length and kernel number per row are important and complex yield-related traits, and many QTLs typically control them. Currently, only two ear-length QTLs have been cloned, which are KNR6 and qEL7/ZmACO2, and published by Prof Zuxin Zhang's lab at Huazhong Agricultural University (HZAU). Prof Jianbing Yan's lab, also from HZAU, recently published another ear length QTL in New Phytologist named YIGE1. YIGE1 was identified by ear length GWAS in 500 diverse inbred lines and fine mapped to a small region by a NIL population. The authors validated YIGE1 gene by Mutator mutants, CRISPR null alleles and transgenic overexpression lines. YIGE1 gene doesn't have a predicted function, but authors found that it can positively control the inflorescence meristem size and spikelet numbers, then moderate ear length and kernel number per row. YIGE1 was proposed to affect ear development by sugar and auxin signal pathways. People may be curious about the gene name YIGE1. Dr. Luo Yun gave birth to her son, Yige, during her PhD work identifying and cloning this gene. She named the gene after her son! Lei Liu, 2022

Luo, Y, et al. 2021. New Phytol. 0:doi: 10.1111/nph.17882
   Genetic variation in YIGE1 contributes to ear length and grain yield in maize
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Wang, YL, et al. 2021. Plant J. 0:doi: 10.1111/tpj.15609
   Genetic variations in ZmSAUR15 contribute to the formation of immature embryo-derived embryonic calluses in maize

The embryos of diverse inbred maize lines differ greatly in their ability to form embryonic calluses (EC). Embryonic calluses, also called type-II callus, are the type of callus used in maize genetic transformation. Using an association panel, Wang et al. explored the embryonic callus inducibility rates (ECIR) and classified inbreds based on high (high-ECIR) and low (low-ECIR) inducibility. The sequence of 16 candidate genes, from previous research, were examined for variation. ZmSAUR15 was the only gene whose sequence showed variation in the CDS and promoter between the two inducibility groups. Transforming both these CDS into Arabidopsis did not alter callus inducibility or callus phenotypes. Measuring mRNA abundance in maize callus showed reduced expression of ZmSAUR15 in high-ECIR. Auxin, as IAA, was then measured and showed higher levels in high-ECIR when compared to low-ECIR. Application of auxin biosynthesis inhibitors reduced inducibility in high-ECIR. To further test the genetics of ZmSAUR15, transgenic overexpression of ZmSAUR15 in high-ECIR reduced callus inducibility, whereas Mu-insertion mutants in W22 (a low-ECIR) increased inducibility. These data all suggest ZmSAUR15 is a negative regulator of type-II callus and is connected to auxin. This work is important because it further explains why some maize inbred lines are resistant to transformation. There is potential to incorporate ZmSAUR15 in transformation protocols to overcome this recalcitrance, allowing for transformation of all inbred lines. Lander Geadelmann, 2022

saur15 = Zm00001d001964

Wang, YL, et al. 2021. Plant J. 0:doi: 10.1111/tpj.15609
   Genetic variations in ZmSAUR15 contribute to the formation of immature embryo-derived embryonic calluses in maize
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Blavet, N, et al. 2021. Proc Natl Acad Sci, USA. 118:e2104254118
   Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution

Blavet and colleagues (2021) generated a pseudomolecule assembly of the maize supernumerary B chromosome. The B chromosome is dispensable and present in only some individuals. Yet it is able to persist through a drive mechanism with two parts: nondisjunction at the second pollen mitosis and preferential fertilization. Classical cytogenetic work has described many properties of the B chromosome, but with this assembly, the researchers attempted to discover the molecular basis of its drive. In their assembly, 1,781 genes were annotated and after TE-related genes were filtered, 758 genes remained. These genes are lowly expressed, but GO terms were enriched for categories that may be related to the drive mechanism and thus possibly selected for B chromosome maintenance. The centromere was similar in structure and function to A chromosome centromeres. They found that the cis-acting factor for nondisjunction is likely the ZmB repeats specific to the B centromere. They were able to narrow down the trans-acting factor for nondisjunction to a 2.7Mb region at the tip of the long arm, but it is unclear if it is one of the 34 predicted genes or a non-genic locus in the region. The factor responsible for preferential fertilization was narrowed down to 8.7Mb area in the pericentromeric region. This is likely to maintain tight linkage with the cis-acting factor for nondisjunction so that the two aspects of the drive mechanism are unlikely to be separated by recombination. They were unable to identify a region in the A chromosomes that could have been the progenitor of the B chromosome. Thus the authors suggest that the B chromosome is the result of gradual transposition of genetic content from A chromosomes where only genes related to the drive mechanism are maintained and the rest deteriorate under relaxed purifying selection. This assembly provides a vital resource for further investigations of the genetics and evolution of the B chromosome. Samantha Snodgrass, 2021

Blavet, N, et al. 2021. Proc Natl Acad Sci, USA. 118:e2104254118
   Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution
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Birdseye, D , et al. 2021. Proc Natl Acad Sci, USA. 118:e2109332118
   Plant height heterosis is quantitatively associated with expression levels of plastid ribosomal proteins

Other ribosomal protein genes whose expression heterosis values were measured: Zm00001d011993 Zm00001d012353 Zm00001d012998 Zm00001d014153 Zm00001d015204 Zm00001d016072 Zm00001d018096 Zm00001d018412 Zm00001d019898 Zm00001d025616 Zm00001d028153 Zm00001d028702 Zm00001d029201 Zm00001d034724 Zm00001d034808 Zm00001d043972

Heterosis, or hybrid vigor, improves the quality and resilience of crops and is widely exploited in agriculture. However, the underlying molecular mechanisms of this phenomenon remain largely unknown. In addition, previous work has shown that ethylene may be involved in heterosis. To identify biomarkers related to hybrid vigor, the authors analyzed paired transcriptome and proteome data of seedling and adult leaf tissue from hybrid maize plants and their inbred parents (B73 and Mo17). They found that expression ratios positively correlated with chloroplast ribosomal proteins and that increased expression of these proteins in hybrid seedling leaves is mediated by ethylene biosynthesis enzymes. They show that the over-expression of chloroplast ribosomal proteins in seedlings quantitatively predicts heterosis traits in adults. They also found evidence that this is conserved in both dicots and monocots. Brianna Griffin, 2021

Proteomics data have been deposited in the Mass Spectrometry Interactive Virtual Environment (accession no. MSV000085916), and anonymized transcriptomics data have been deposited in the NCBI SRA (accession no. PRJNA747924).

Heterosis is one of the most important biological questions yet still remains obscure. Hybrid vigor can be defined as multiple aspects, including numerous trait advantages, physiological differences, as well as transcriptome and proteome changes. Birdseye et al. reported a comprehensive proteome comparison using seedling leaves from maize hybrids and their corresponding parents. They quantitatively assessed the proteins that showed non-additive effect expression in hybrids, and found many are related to the nuclear- and plastid-encoded subunits of complexes that are required for protein synthesis in the chloroplast and for the light reactions of photosynthesis. Particularly intriguingly, there is a strong correlation between plant height heterosis and plastid ribosomal proteins abundance. However such correlation was barely found between plant height heterosis and transcription, suggesting a discordance between the transcripts and protein expression in hybrids. Based on the previous report that ethylene biosynthetic enzymes were expressed below midparent levels in the Arabidopsis hybrids, the authors also confirmed a conserved pattern in maize. Maize ethylene biosynthesis double mutant Zmacs2/6 largely phenocopied the hybrid proteome, in terms of the increased expression of chloroplast ribosomal proteins. Overall, this report concluded an interesting module that links the ethylene biosynthesis and the accumulation of the ribosomal protein, and both of them may directly contribute to the heterosis physiology. Zhaobin Dong, 2021

Birdseye, D , et al. 2021. Proc Natl Acad Sci, USA. 118:e2109332118
   Plant height heterosis is quantitatively associated with expression levels of plastid ribosomal proteins
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Gong, P, et al. 2021. Plant Physiol. 0:doi: 10.1093/plphys/kiab514
   SAMBA controls cell division rate during maize development

Other genes encoding APC enriched proteins: GRMZM2G089296 GRMZM2G170591 GRMZM2G168886 GRMZM2G053766 GRMZM2G053980 GRMZM2G012220 GRMZM2G431251 GRMZM2G054247 GRMZM2G354696 GRMZM2G020201 GRMZM2G166684 GRMZM2G147603 GRMZM5G821639 GRMZM2G149717 GRMZM2G314647 GRMZM2G077183 GRMZM2G143480 GRMZM2G439339 GRMZM2G092910 GRMZM2G072156 GRMZM2G460860 GRMZM2G360677 GRMZM2G180724 GRMZM2G132847 GRMZM2G472346 GRMZM2G041765 GRMM2G033644 GRMZM2G411084 GRMZM2G142111 GRMZM2G099355 GRMZM2G145599 GRMZM2G032267 GRMZM5G862331 GRMZM2G161619 GRMZM5G829955

During the cell cycle process, specific proteins are targeted by E3 ubiquitin ligase and degraded through 26S proteasome. Anaphase promoting complex (APC/C) is well studied E3 ligase in plants during cell division. In this study, Gong et al. studied SAMBA, negative regulator of APC/C and direct interactor of APC3b in the dicot Arabidopsis thaliana, in the monocot system, maize. CRISPR/Cas9 edited samba mutant alleles have reduced internode, sheath, blade length, and blade width. Further cellular investigation suggested that samba-1 has smaller cells and reduced cell cycle duration compared to wild type in leaf. Gong et al. simulated the CRISPR/Cas9 truncated version of different samba allele to test their interaction with APC3 and found that the truncated versions have SAMBA function remaining and can interact with APC3. Altogether, this study highlighted the conserved role of SAMBA in Maize, similar to Arabidopsis, in cell cycle regulation. Arif Ashraf, 2021

Gong, P, et al. 2021. Plant Physiol. 0:doi: 10.1093/plphys/kiab514
   SAMBA controls cell division rate during maize development
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Zhou, P, et al. 2021. Plant Cell. 0:doi: 10.1093/plcell/koab267
   Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information

Many genes are differentially expressed in response to different abiotic stresses. Some of these genes harbor regulatory elements, which can control the expression of these genes. Although several research developed predictive models to predict gene expression in response to stress using putative cis-regulatory motifs, whether these predicted models can be applied to different genotypes have not been well studied. Zhou and his collaborators profiled and compared the transcriptome of three inbreds (B73, Mo17 and W22) and their hybrids (B73xMo17, W22xB73 and W22xMo17) responsive to heat and cold stress at different time points after the treatments of heat and cold. Their data demonstrated many examples of cis- and trans-regulatory variation that result in varied expression responses to heat or cold stress. They further used these cis-regulatory variation information particularly motifs enriched near the transcription start sites in the promoter regions to generate predictive models to predict gene expression responses across different genotypes. They also demonstrated that the insertion/deletion polymorphisms or other structural variants that create presence/absence of key motifs are important for variable responses in different genotypes. This research provides insights into the understanding how variation among cis-regulatory elements drives variation for gene expression in response to stress in different genotypes of crop species. Meixia Zhao, 2021

Zhou, P, et al. 2021. Plant Cell. 0:doi: 10.1093/plcell/koab267
   Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information
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Wurschum, T, et al. 2021. Theor Appl Genet. 0:doi: 10.1007/s00122-021-03963-3
   High-resolution association mapping with libraries of immortalized lines from ancestral landraces

Wurschum and colleagues (2021) demonstrate the possibilities of using immortalized double haploid libraries of maize landraces as mapping populations for quantitative traits. Landraces contain a cornucopia of genetic diversity and are highly adaptive in their home range. While landraces provide a reservoir of highly adaptive alleles, it can be difficult to use them in mapping populations without confounding artifacts due to maladaptive testing environments or population structure, similar to issues facing other diverse mapping populations. The authors argue immortalized double haploid libraries resolve these issues by capturing more of the diversity of a landrace within a library of lines, removing population structure, and avoiding issues of large differences in adaptation to the test environment. They go on to demonstrate the capability of this approach by using an immortalized doubled haploid population of six European Flint landraces to map high resolution QTL for oil content and allatoin content, a metabolite within the purine recycling pathway. They reproduce previously reported findings of a polymorphism at DGAT1-2 that is strongly associated with oil content. They also uncover promoter and coding region variants in a QTL including the gene allantoinase which are strongly associated with allantoin content. Further investigation suggests the promoter variants may explain most of the variation, but that different combinations of polymorphisms between the promoter and coding regions may also alter allantoin content. Wurschum and colleagues (2021) conclude by enumerating best practices for generating and using immortalized libraries of landraces for future mapping populations. Samantha Snodgrass, 2021

For oil content, DGAT1-2 (gene symbols: Zm00001d036982, GRMZM2G169089, LOC103629820) For allantoin/the allantoinase (gene symbols:Zm00001d026635, GRMZM2G173413, LOC100274212).

Wurschum, T, et al. 2021. Theor Appl Genet. 0:doi: 10.1007/s00122-021-03963-3
   High-resolution association mapping with libraries of immortalized lines from ancestral landraces
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Ning, Q, et al. 2021. Nature communications. 12:5832
   An ethylene biosynthesis enzyme controls quantitative variation in maize ear length and kernel yield

Maize ear length is one of the most important traits for the yield, yet little is known about the genetic basis for its complex development. Here Ning et al identified an ethylene biosynthesis gene that surprisingly controls ear length and can improve yield in hybrids. By fine-mapping a previously isolated QTL, the authors confirmed variations in the promoter of a 1-aminocyclopropane-1-carboxylate oxidase2 (ACO2) gene contributed to the ear length phenotype. ACO2 functions in the last step of ethylene biosynthesis, and this function was further found to negatively control ear length and grain yield, probably through manipulating the ethylene homeostasis to affect floret number and fertility in developing ears. Nevertheless, it should be noted that other phytohormones, such as auxin and JA, as well as a few inflorescence development genes, may also cross-talk with ethylene in this process. Lastly, gene editing of ACO2 promoted flower development, affected spikelet number, floral fertility, ear length and kernel number, eventually leading to an impressive increase in grain yield in hybrid lines. Zhaobin Dong, 2021

Gene: ZmACO2 = Zm00001d020686

Ning, Q, et al. 2021. Nature communications. 12:5832
   An ethylene biosynthesis enzyme controls quantitative variation in maize ear length and kernel yield
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Qin, XN, et al. 2021. Molecular Plant. 0:doi: 10.1016/j.molp.2021.10.001
   Main restorer Rf3 for maize S type cytoplasmic male sterility encodes a PPR protein that functions in reduction of the transcripts of orf355

Male-sterile lines, especially cytoplasmic male sterile (CMS) lines, are extensively used in commercial hybrid seed production. However, the genetic basis of fertility restoration for CMS, especially the S type CMS (CMS-S) remains exclusive. In 1978, Laughnan and Gabay mapped the main restorerof CMS-S, Rf3, to the long arm of chromosome 2. In this study, Qin and its colleagues further mapped Rf3 to a region of 220 kb using S-Mo17rf3rf3/Ye107//Mo17rf3rf3 backcross population. PPR proteins, PPRK1 and PPRK2, are the candidate genes. Transgenic analysis showed that PPRK2 is the candidate of Rf3.The transcription and Electrophoretic Mobility Shift Assays suggest that mitochondria-targeted PPRK2 could interact with orf77, suppress the editing and degradation of orf77, accelerate the cleavage rate of orf355 by an unknow mechanism, and eventually restored the fertility of CMS-S. Yanfang Du, 2021

Genes: PPRK1 = Zm00031a017460, and PPRK2 = Zm00031a017461

Qin, XN, et al. 2021. Molecular Plant. 0:doi: 10.1016/j.molp.2021.10.001
   Main restorer Rf3 for maize S type cytoplasmic male sterility encodes a PPR protein that functions in reduction of the transcripts of orf355
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Cheng, CY, et al. 2021. Nature communications. 12:5627
   Evolutionarily informed machine learning enhances the power of predictive gene-to-phenotype relationships

Cheng et al. used evolutionarily conserved gene expression datasets within and across species to create a machine learning model that predicts nitrogen use efficiency (NUE) genes in maize and Arabidopsis. They also applied this model to previously published transcriptome/phenotype datasets in rice and mouse. The authors validate the model by functionally characterizing seven candidate transcription factors in maize and Arabidopsis. The machine learning pipeline integrates phenotype, transcriptome data, genetic variation, and environmental responses to; 1. preselect subsets of transcripts based on conserved transcriptome data within and across species, 2. Use this conserved data as a biologically based way to improve the machine learning model, and 3. Rapidly validate the function of "important gene features". This study is significant because it shows that using an evolutionarily conserved dataset for machine learning allows a biologically principled method to improve the predictive power of genotype to phenotype. The authors emphasize the power of their method and state that this work could be applied to biological, agricultural, and medical trials to uncover genes involved in complex phenotypes. Brianna Griffin, 2021

"The curse of dimensionality", i.e. too many predictors compared with the number of observations, causes overfitting in machine learning. This problem is especially severe when predicting phenotypes using molecular markers as predictors. To reduce the number of predictors, an alternative approach is to use molecular phenotypes (such as gene expression levels) as predictors. However, the number of genes is still often far more than the number of observations. In this study, the authors used gene expression levels to predict nitrogen use efficiency (NUE). To reduce the number of genes, inter- or intra-species conserved nitrogen-responsive genes where chosen as predictors. They showed that evolutionarily informed feature selection effectively reduced the dimensionality of predictors, and ultimately improved the predictive accuracies in some genetic backgrounds, although this model cannot predict which genetic background would perform better in NUE (Fig. 5, Step 3). The authors further functionally validated several candidate transcription factors with predictive power for NUE, demonstrating the power of this approach to uncover novel genes controlling NUE. Hai Wang, 2022

Cheng, CY, et al. 2021. Nature communications. 12:5627
   Evolutionarily informed machine learning enhances the power of predictive gene-to-phenotype relationships
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Stitzer, MC; Anderson, SN; Springer, NM; Ross-Ibarra, J. 2021. PLoS Genetics. 17:e1009768
   The genomic ecosystem of transposable elements in maize

Transposable elements (TEs) constitute a large proportion of the sequences of many plant genomes, particularly maize, of which more than 85% of the genome can be ascribed to these repetitive elements. TEs are an important source of both genetic and epigenetic variation in plants. However, because of their repetitive nature and their diversity, TEs pose a serious challenge to genome annotators, making it difficult to detect that variation. Stitzer and her collaborators updated us with a comprehensive TE annotation in the maize genome, which contains 341,426 structural TE copies in 27,444 families of the 13 superfamilies. These TEs vary in length, age, base composition, insertion location, distance to the nearest gene, coding capacity, expression, methylation, and many other features. Furthermore, they modeled the relationship between attributes of the genomic environment and the survival of TE copies and families, and demonstrated that TE transposition is highly family- and context-dependent. Overall, this TE database would be very valuable to the maize community to not only work on genetic and epigenetic regulation of TEs, but also many other research such as dissection of their effects on genetic and phenotypic diversity. Meixia Zhao, 2021

Stitzer, MC; Anderson, SN; Springer, NM; Ross-Ibarra, J. 2021. PLoS Genetics. 17:e1009768
   The genomic ecosystem of transposable elements in maize
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Julius, BT, et al. 2021. Plant Cell. 0:doi: 10.1093/plcell/koab193
   Maize brittle stalk2-like3, encoding a cobra protein, functions in cell wall formation and carbohydrate partitioning

Julius et al. identified two carbohydrate partitioning defective (cpd) mutants, cpd28 and cpd47, from an EMS-mutagenized population based on plant height, leaf chlorosis, and anthocyanin as phenotypes. Both cpd28 and cpd47 accumulate more carbohydrates in leaves due to the reduction of sucrose export from leaves. Interestingly, authors observed that apart from carbohydrate-related phenotype, both cpd28 and cpd47 mutants have shorter root compared to wild-type and exogenous sucrose in the media cannot help to recover the root growth defect. Their bulked segregant analysis (BSA) indicated that the cpd28 and cpd47 mutants are result of mutations in a single gene, Brittle Stalk2-like3 (Bk2L3). ZmBk2L3 is part of maize COBRA gene family and localizes on the plasma membrane. ZmBk2L3 is closely similar to its Arabidopsis and rice counterpart. Furthermore, bk2l3 mutant has cellulose deficiencies and consequently, cell wall defects. Arif Ashraf, 2021

Bk2L3 = Zm00001d034049

Julius, BT, et al. 2021. Plant Cell. 0:doi: 10.1093/plcell/koab193
   Maize brittle stalk2-like3, encoding a cobra protein, functions in cell wall formation and carbohydrate partitioning
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Lozano, R, et al. 2021. Nature Plants. 7:17-24
   Comparative evolutionary genetics of deleterious load in sorghum and maize

Lozano et al (2021) demonstrate the potential to improve functional annotations of a species by leveraging information from phylogenetically related species with more extensive genetic resources. They use existing maize resources (1,218 maize lines) and generate genome-wide markers for sorghum (499 lines) spanning wild relatives, landraces, and modern lines. Variants in coding regions were assigned into deleterious categories based on GERP and SIFT scores, which estimate the amount of constraint acting on a nucleotide and effect of amino acid substitution on protein function respectively. While both sorghum and maize showed decreased nucleotide diversity from wild to landrace to modern lines, maize deleterious load increased with domestication unlike sorghum which decreased. This decrease of load in sorghum was not related to the decrease of nucleotide diversity (pi) or introgression from wild relatives into modern lines. Using a simulation model, Lozano and colleagues suggest the main driver behind sorghum's decreased load is the increase in self pollination in domesticates relative to wild lines (7-20% outcrossing compared to 70% respectively). Lozano and colleagues also tested the use of convolutional neural network (CNN) models in predicting the average SIFT and syntenic identity of sorghum genes. Average SIFT was best predicted by average GERP score, the number of variants within the CDS, and RNA expression variance in both maize and sorghum, likely representing the strength of purifying selection at the locus and reiterating known expression dysregulation patterns associated with rare-allele burden. Syntenic identity was best predicted using ssw, a metric of alignment between sorghum and maize, and maize nucleotide diversity (pi), which reiterates known characteristics of syntenic loci. Altogether, this work suggests how maize and other model species could inform functional annotations in related systems. Samantha Snodgrass, 2021

Lozano, R, et al. 2021. Nature Plants. 7:17-24
   Comparative evolutionary genetics of deleterious load in sorghum and maize
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Su, HH, et al. 2021. J Exp Bot. 0:doi: 10.1093/jxb/erab364
   Identification of ZmNF-YC2 and its regulatory network in maize flowering time

Flowering time is an important agronomic trait that determines the distribution and adaptation of crop, especially in the maize breeding. A set of genes including ZmCCT9/10, Zea mays CENTRORADIALIS 8 (ZCN8), FLO/LFY homologs (ZFL), DELAYED FLOWERING 1 (DLF1), ZMM4 and ZmMADS1 have been reported in controlling maize flowering time. In this study, Yanhui Chen group cloned a NF-Y subunit encoding gene, ZmNF-YC2, that regulating flowering time positively, from the qDPS10-2 quantitative trait locus (QTL) through positional cloning and fine-mapping. They developed a gene model of flowering time regulation in maize that ZmNF-YC2 promotes the expression of ZmNF-YA3, ZmNF-YA3 suppresses the transcription of ZmAP2, and ZmAP2 targets on ZMM4 to modulate flowering time, the model could be used for maize breeding by improving flowering time. Yanfang Du, 2021

Genes: ZmNF-YC2 (Zm00001d024230), ZmNF-YA3 (Zm00001d042968), ZmAP2 (Zm00001d002075), ZMM4 (Zm00001d034045)

The data that support the findings of this study are openly available in the NCBI Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra). The BioProject and SRA accession number is PRJNA730925.

Su, HH, et al. 2021. J Exp Bot. 0:doi: 10.1093/jxb/erab364
   Identification of ZmNF-YC2 and its regulatory network in maize flowering time
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Pokhrel et. al. 2021. Nature communications. 12:4941
   Pre-meiotic 21-nucleotide reproductive phasiRNAs emerged in seed plants and diversified in flowering plants

Phased small interfering RNAs (phasiRNAs) are a class of 21 and 24 nt siRNAs that are triggered by microRNAs and subsequently processed into secondary siRNAs to regulate many loci in plant genomes. Previous research has reported that 21 nt reproductive phasiRNAs triggered by miR2118 are highly enriched in pre-meiotic anthers in multiple monocot species, such as maize and rice. However, these 21 nt reproductive phasiRNAs are not observed in some well-studied eudicot families including the Brassicaceae, Solanaceae and Fabaceae. This led to the conclusion that this pathway is absent in eudicots. Pokhrel and his collaborators investigated small RNAs in several eudicots: strawberry, rose, the basal eudicot columbine, and flax, and find that these phasiRNAs also exist in these eudicots but with new miRNA triggers miR11308 and miR14051. Further investigation of the location of the miRNA triggers indicates that unlike miR2118 in maize and rice, which localizes to the epidermis, miR11308 localizes in microspore mother cells, meiocytes, and tapetal cells in strawberry. They proposed that 21 nt reproductive phasiRNAs are a more fundamental and broadly conserved pathway, which may emerge in gymnosperms but were lost in some eudicot lineages probably due to accommodations or adaptations of development. Overall this research shows the conservation of 21 nt reproductive phasiRAs in seed plants and suggests a functional role in reproduction. Meixia Zhao, 2021

Pokhrel et. al. 2021. Nature communications. 12:4941
   Pre-meiotic 21-nucleotide reproductive phasiRNAs emerged in seed plants and diversified in flowering plants
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Xu, XS, et al. 2021. 56:1-12
   Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery

Single-cell RNA sequencing (scRNA-seq) provides the opportunity to investigate gene expression at a very high resolution. Xu and his colleagues performed scRNA-seq technology and constructed a high-resolution transcriptome atlas of the 5-10 mm developing maize ear inflorescence. They investigated the transcriptional profiles of 12,525 single cells from developing maize ears and predicted 12 meta-clusters that were mostly associated with meristem. This scRNA-seq atlas has been utilized to distinguish redundant from non-redundant paralogs involved in gene networks, build transcriptional regulatory networks, and identify genes associated with maize yield traits. Furthermore, they validated their results by mRNA in situ hybridization and by fluorescence activated cell sorting RNA-seq. Their single-cell gene co-expression networks will facilitate developmental genetics studies by predicting genetic redundancy, integrating transcriptional regulatory networks, and ultimately facilitate maize breeding by identifying candidate genes associated with crop yield traits. This single-cell transcriptome atlas is a valuable resource for the maize community. Meixia Zhao, 2021

Xu et al. map the transcriptional landscape of 12,525 single cells from developing maize ears to create a developmental atlas that shows single-cell RNA-seq map of the inflorescence. This was validated via in situ hybridization and florescence-activated cell sorting (FACS) RNA-seq. The authors also predicted 12 meta-clusters using known markers. With these clusters they found distinct subclusters for meristem, branching, xylem, phloem, determinate lateral organs, and ground tissues. The authors highlight their ability to accurately predict redundancy in a family of maize TPPs that control inflorescence branching. They also show that scRNA-seq marker genes are associated with maize ear traits from GWAS. This study is significant because it is an incredibly useful tool for facilitating genetic studies and breeding strategies. Brianna D. Griffin, 2021

Xu, XS, et al. 2021. 56:1-12
   Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery
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Zeng, R, et al. 2021. Nature communications. 12:4713
   Natural variation in a type-A response regulator confers maize chilling tolerance

Other differentially expressed genes: Zm00001d038863 Zm00001d0034723 Zm00001d0003190 Zm00001d0018701 Zm00001d005451 Zm00001d009567 Zm00001d005775 Zm00001d035899 Zm00001d047694 Zm00001d041844

Maize (Zea mays L.), as a tropical region originated crop, is generally sensitive to low temperatures. In spite of the fact that improvement of chilling tolerance is critical for its growth expansion at higher latitudes, the genetic basis of chilling adaption in maize remains obscure. In this report, Zeng et al. identified a type-A response regulator that modulates low-temperature tolerance in maize. Through a comprehensive phenotype screening of transgenic maize lines overexpressing over 700 genes, the authors isolated one of them, ZmRR1 overexpression, enhanced chilling tolerance. in accordance with that, ZmRR1 mutants generated by CRISPR showed more vulnerable by the chilling stress, demonstrating that ZmRR1 functions positively in regulating chilling tolerance. More importantly, ZmRR1 locus based association analysis using natural diversity lines population was performed, and two haplotype groups, HapA and HapB, were designated as resistant and susceptible alleles of ZmRR1, respectively. The most significant association marker was an InDel contains mitogen-activated protein kinase (MPK) phosphorylation residue within the ZmRR1 coding region, and indeed HapB could be phosphorylated whereas this phosphorylation does not occur in the HapA variant. The authors then identified ZmMPK8 interacts and phosphorylates HapB. In contrast, ZmMPK8 interact with HapA at a lower affinity, but showing no detectable phosphorylation activity. The phosphorylation by ZmMPK8 on ZmRR1 HapB was further characterized, and it was found to promote the ubiquitin-mediated degradation of ZmRR1 under cold stress. As expected, evidence from overexpression and knock-out mutants for ZmMPK8 confirmed that this gene negatively regulated chilling tolerance. At last, other putative chilling tolerance regulators were characterized, including ZmDREB1 and ZmCesA family genes, the expression of which are positively (and likely indirectly) modulated by ZmRR1. This is a stellar work that elucidates a novel pathway underlying such a complex trait, and these findings could be useful genetic resource for manipulating chilling tolerance in crops. Zhaobin Dong, 2021

Zeng, R, et al. 2021. Nature communications. 12:4713
   Natural variation in a type-A response regulator confers maize chilling tolerance
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Pedroza-Garcia, JA, et al. 2021. Plant Cell. 0:doi: 10.1093/plcell/koab158
   Maize ATR safeguards genome stability during kernel development to prevent early endosperm endocycle onset and cell death

DNA damage response (DDR) depends on two major components, Ataxia-telangiectasia mutated (ATM) and ATM and Rad3-related (ATR). In this study, Pedroza-Garcia et al. tried to understand the functional conservancy or divergence of these two genes in maize. Authors generated CRISPR/cas9-induced mutant lines, Zmatr and Zmatm, for ATR and ATM in maize. Using Zmatr and Zmatm mutant lines, they have found that Zmatr, not Zmatm, is hypersensitive to hydroxyurea (HU), a replicative stress inducer. But, both Zmatr and Zmatm are sensitive to zeocine, a radiomimetic drug, and ℽ-irradiation-mediated DNA damage. Further cell biology study suggested that Zmatr and Zmatm are unable for DNA repair and activation of checkpoint after HU and zeocine treatment. Additionally, Zmatr has defective kernel due to premature endoreduplication in the endosperm. Altogether, this study pointed out the partially conserved function of ATM and ATR in maize compared to Arabidopsis. Arif Ashraf, 2021

Genes: Zm00001d014813 (Zmatr), Zm00001d040166 (Zmatm)

Pedroza-Garcia, JA, et al. 2021. Plant Cell. 0:doi: 10.1093/plcell/koab158
   Maize ATR safeguards genome stability during kernel development to prevent early endosperm endocycle onset and cell death
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Savadel, SD, et al. 2021. PLoS Genetics. 17:8
   The native cistrome and sequence motif families of the maize ear

Understanding the transcriptional regulatory networks that orchestrate one biological process requires a complete profile of the transcription factor site-specific binding but also a high-resolution landscape of the accessible chromatin region (ACR). To improve the resolution limit of the current chromatin structure profiling toolkits, Savadel and Hartwig et al. developed an approach termed MNase-defined cistrome-Occupancy Analysis (MOA-seq), and its capability for ACR characterization was well confirmed with high resolution in maize ear tissue. Compared to other strategies such as ATAC seq, the MOA-seq was able to isolate more, smaller, and unique peaks. The MOA footprints were also found to be associated with functional elements, including promoters and long-range chromatin interaction sites around genes with known functions. Thanks to the high resolution of MOA-seq (<30bp), which is about the size of transcription factor bound sequence, this strategy is well performed to predict putative TF footprints and binding motifs genome-wide. Zhaobin Dong, 2021

All Data is in the Supplimentary files

To further elucidate the mechanisms of gene regulation it is important to identify accessible chromatin and specific binding sites of transcription factors (TFs). Savadel et al developed a new "high resolution, high-throughput, genome-wide" method, MOA-seq (MNase-defined cistrome-Occupancy Analysis), to identify TFs at cis-regulatory elements within accessible chromatin regions. This is significant because current methods for identifying and analyzing TFs have many different pitfalls such as lacking scalability or chromatin information, or requiring specific antibodies. In this paper the authors define the cistrome of developing maize ears and show that MOA-seq maps chromatin regions, identifies TF-binding sites, and maps small motifs (~30bp) to produce a multitude of candidate TFs. Using this method, the authors were able to map a cistrome of 145,000 MOA footprints (MFs). When compared to ATAC-seq, the majority of these MFs were novel findings, and ~80% of the ATAC-seq discovered regions were also identified. When compared to ChIP-seq, MOA-seq had ~67% overlap. These MFs were associated with promoter regions and enriched for TF binding and long-range chromatin interaction sites. In addition, MOA-seq identified 215 motif families over 100,000 non-overlapping binding sites across the genome, indicating that this method has a high spatial resolution. This study represents one of the most complete maps of putative TF DNA-binding sites. Brianna Griffin, 2021

Savadel, SD, et al. 2021. PLoS Genetics. 17:8
   The native cistrome and sequence motif families of the maize ear
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Abraham-Juarez, M-J, et al. 2020. Plant Cell. 0:doi: 10.1105/tpc.20.00300
   Evolutionary variation in mads-box dimerization affects floral development and protein abundance in maize

The development of floral organ morphology controlled by the MADS box transcription factors is conversed in many angiosperms, especially the B-class genes, in the regulation of stamen and petal development. The complexes of homologous MADS box proteins specify homologous floral organs in different lineages, and differential MADS box complex assembly presents a model for explaining floral diversification. However, the consequences of changing MADS box protein-protein interactions have not been extensively tested in planta. In this study, Jazmin and her college engineered an ancestral variant of STERILE TASSEL SILKY EAR1 (STS1; a homolog of PISTILLATA in Arabidopsis) that forms both homodimers and heterodimers with SILKY1 (SI1; a homolog of APETALA3 in Arabidopsis), and use the genetics and genomic recourses in maize to determine the functional consequences of evolutionary variation of STS1 dimers. They found that the ancestral variant of STS1 affects downstream gene expression and protein-protein interactions, and subtle, quantitative effects on stamen development, which suggests that small coding sequence variation of MADS-box genes may have affected the gradual evolution on floral development. And using the allelic series provided by evolution to dissect effects of a single base-pair variation is critical in genome editing. Yanfang Du, 2021

Genes: STS1 (Zm00001d042618); SI1 (Zm00001d036425)

Raw sequencing data are available at NCBI SRA under Bioproject PRJNA625570. Supplemental data sets and anther images are available at dryad (https://datadryad. org/stash/dataset/doi:10.5061/dryad.4xgxd2573). Code for analyses and figure generation is available on GitHub (https://github.com/BartlettLab/ B-class).

Abraham-Juarez, M-J, et al. 2020. Plant Cell. 0:doi: 10.1105/tpc.20.00300
   Evolutionary variation in mads-box dimerization affects floral development and protein abundance in maize
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Bornowski, N, et al. 2021. Plant Genome. 0:doi: 10.1002/tpg2.20114
   Genomic variation within the maize stiff-stalk heterotic germplasm pool

Bornowski and colleagues (2021) created de novo, long read assemblies for five stiff stalk inbreds: B84, LH145, NKH8431, PHB47 and PHJ40. B84 comes from the Iowa Stiff Stalk Synthetic breeding program while the rest are ex-PVP lines. The assemblies themselves are of high quality, with 94.5% of reads anchored to chromosomes, high BUSCO scores for gene space contiguity, and high LAI scores for TE space contiguity. Annotations were made using a streamlined pipeline that, when applied to B73v4, greatly reduced the frequency of unsupported isoforms. Comparison across stiff stalk assemblies + Mo17 and PH207 revealed most genes were present in all lines or all stiff stalk lines. Few genes were found only in a single genome. However, genes present in the stiff stalk pangenome were less likely to be found in either Mo17 or PH207 and vice versa. This hints at differing gene content between heterotic pools, but more representation in the non-stiff stalk and Iodent heterotic pools would be needed for confirmation. While predicted proteomes mostly overlapped along with high IBS, structural variants occurred. Deletions were the most common SV, though there were a few large inversions. Given the importance of the stiff stalk heterotic pool in historic and modern maize breeding, it is important to explore the genetic and genomic diversity identified through these assemblies, especially since this diversity has persisted despite this germplasm originating in a highly selected environment. Samantha Snodgrass, 2021

Bornowski, N, et al. 2021. Plant Genome. 0:doi: 10.1002/tpg2.20114
   Genomic variation within the maize stiff-stalk heterotic germplasm pool
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Hufford, MB, et al. 2021. Science. 0:doi: 10.1126/science.abg5289
   De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

An a-maize-ing set of genomes: Maize is an important crop that is cultivated worldwide. As maize spread across the world, selection for local environments resulted in variation, but the impact on differences between the genome has not been quantified. By producing high-quality genomic sequences of the 26 lines used in the maize nested association mapping panel, Hufford et al. map important traits and demonstrate the diversity of maize. Examining RNA and methylation of genes across accessions, the authors identified a core set of maize genes. Beyond this core set, comparative analysis across lines identified high levels of variation in the total set of genes, the maize pan-genome. The value of this resource was further exemplified by mapping quantitative traits of interest, including those related to pathogen resistance. Laura M. Zahn, Science magazine Editor, 2021

Maize is a plant species with extreme genetic diversity. However, most current genomic resources are referenced to a single inbred line, B73. Hufford and his colleagues and collaborators sequenced 25 founder inbred lines of the maize nested association mapping (NAM) population, which has been used to map the genetic basis of many quantitative traits. They sequenced, assembled and annotated genomes for these 25 NAM founder inbreds and an improved reference assembly of B73. They identified a total of 103,033 pan-genes across the 26 genomes, and out of these, 32,052 (31.1%) genes are in the core or near-core portion of the pan genome. In addition to genes, they also identified repetitive sequences including transposable elements and tandem repeat arrays, and detected a substantial number of structure variations among these founder inbred lines, which may contribute to phenotypic variation. Furthermore, they discovered some candidate cis-regulatory elements through DNA methylation sequencing, and demonstrate that DNA methylation level also varies among these inbred lines. Analysis of retention of genes in the two maize subgenomes among these 26 genomes with sorghum suggests that biased fractionation is ongoing in the maize population. Overall, the sequences, annotation and comparative analysis of these 26 genomes will have broad utility for genetic and genomic studies and facilitate rapid association to phenotyping information. These data will be very useful and valuable for the entire maize community. Meixia Zhao, 2021

Hufford, MB, et al. 2021. Science. 0:doi: 10.1126/science.abg5289
   De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
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Schneider, HM, et al. 2021. Plant Cell Environ. 0:doi: 10.1111/pce.14135
   Root angle in maize influences nitrogen capture and is regulated by CBL-interacting serine/threonine-protein kinase 15 (ZmCIPK15)

Root architecture defines the capacity of plants for their nutrient uptake. In this study, Schneider et al. examined 481 genotypes from the Wisconsin Diversity (WiDiv) panel for measuring root angle. Based on their GWAS (Genome-wide Association Study) analysis, they have narrowed down to the gene Zm00001d033316, which encodes CBL-interacting serine/threonine-protein kinase and express prominently in the root, for functional analysis of root angle and nutrient acquisition. For the further functional analysis, authors used ZmCIPK15 mutant (mu1046464) and tested the homozygous mutant plants in both greenhouse and six different field environments, including high and low nitrogen availability and well-watered and water deficient as well. cipk15 mutant has steeper root growth angle and this steeper angle helps to have higher nitrogen acquisition, as well as higher shoot biomass, in the low nitrogen environment. Additionally, Schneider et al. used in silico simulation using OpenSimRoot to demonstrate that steeper root angle of cipk15 mutant facilitates higher nitrogen capture. Arif Ashraf, 2021

Gene: ZmCIPK15 (Zm00001d033316)

Schneider, HM, et al. 2021. Plant Cell Environ. 0:doi: 10.1111/pce.14135
   Root angle in maize influences nitrogen capture and is regulated by CBL-interacting serine/threonine-protein kinase 15 (ZmCIPK15)
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Ding, YZ, et al. 2020. Nature Plants. 0:doi: 10.1038/s41477-020-00787-9
   Genetic elucidation of interconnected antibiotic pathways mediating maize innate immunity

Further elucidating biosynthetic pathways involved in innate immunity is crucial to gaining deeper insight into biochemical defense responses and crop resistance genes. To better understand maize antibiotic biosynthesis, an important aspect to pathogen defense, the authors identified 17 metabolites that are products of the zealexin pathway, a family of metabolites previously indicated in biochemical fungal pathogen resistance. The authors used a combination of multi-omics, biochemical and genetic techniques and ultimately characterized 10 genes in three distinct clusters that result in the production of 17 zealexin pathway metabolites and produce antibiotic effects. Their results suggest that sesquiterpenoids mediate maize disease resistance and that zealexins are major antibiotics involved in innate immunity. Brianna Griffin, 2021

Ding, YZ, et al. 2020. Nature Plants. 0:doi: 10.1038/s41477-020-00787-9
   Genetic elucidation of interconnected antibiotic pathways mediating maize innate immunity
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Zhang, YC, et al. 2021. PeerJ Life and Environment. 9:e11707
   Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize

Genes mentioned explicitly (B73v4 annotation): Zm00001d010454, Zm00001d010458, Zm00001d010459, and Zm00001d050021

Zhang et al 2021 set out to map the genetic architecture of five maize germination traits under cold stress to identify targets for breeding seedling cold tolerance. They used a diverse panel of 300 Chinese inbred lines, 30 of which had been used to develop commercial varieties in elite breeding programs, to conduct a FarmCPU model GWAS on these traits. They found 15 significant SNPs. Alleles associated with an increased trait value were considered favorable. Within the 30 lines that influenced commercial pools, the frequency of each favorable allele varied widely (10% - 97%) and the stacking of alleles also varied (27% - 60% of the 15 favorable alleles found in a line), suggesting potential to improve breeding programs. Of the 15 SNPs, three were associated with multiple traits. Ten gene models (B73v4 annotation) were linked to these three SNPs, only six of which had functional annotations. Zhang and colleagues further narrowed their pool of candidate genes by looking for variants in the gene bodies or promoter regions (2kb upstream of the TSS) and correlated them with chilling germination. This resulted in four candidate genes: Zm00001d010454, Zm00001d010458, Zm00001d010459, and Zm00001d050021. qRT-PCR of these candidates under control and cold stress conditions with chilling sensitive and chilling tolerant lines revealed dynamic responses in expression levels between conditions and lines over a 120 hour period. Understanding the genetic architecture of maize seedling cold response and targeting favorable alleles for breeding could lead to improved yields in temperate or montane environments as cold snaps early in the growing season can have significant impacts on yield. Samantha Snodgrass, 2021

Zhang, YC, et al. 2021. PeerJ Life and Environment. 9:e11707
   Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize
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Tang, B, et al. 2021. J Exp Bot. 0:doi: 10.1093/jxb/erab254
   Natural variations in the P-type ATPase heavy metal transporter ZmHMA3 controlling cadmium accumulation in maize grains

Cadmium (Cd) pollution to the agricultural soil has been a serious global issue due to the increasing industrial and agricultural activities. In this study, Tang et al identified that natural variation on a heavy metal ATPase gene ZmHMA3 is responsible for the different Cd accumulation in grains among maize inbred lines. Through GWAS analysis of 513 maize accessions, two loci on Chr 2 were detected to be significantly associated with grain Cd accumulation. Three candidate genes within were proposed as the causative for the Cd trait, including GRMZM2G175576 ZmHMA3 and GRMZM2G455491 (ZmHMA4), as the Arabidopsis and rice homologs have been shown to function in sequestering Cd in cell vacuoles. Meanwhile, an F2 mapping population has also been generated by crossing Jing724 as a low-Cd line with a high-Cd line Mo17. Fine mapping narrowed down the major QTL to a 232 kb interval contains ZmHMA3 and ZmHMA4, consistent with the GWAS results. By the evidence from genomic structural variation, gene expression and mutant analysis, ZmHMA3 rather than ZmHMA4 was confirmed as the functional gene for the Cd accumulation in maize grains. Lastly, PCR-based molecular markers were developed and used to distinguish five haplotypes with different grain Cd contents in the GWAS panel, showing a promising application in the marker-assisted selection for elite maize varieties with low grain Cd. Zhoabin Dong, 2021

GRMZM2G175576 (ZmHMA3) GRMZM2 G455491 (ZmHMA4) GRMZM2G018241 (ZmCESA9)

Tang, B, et al. 2021. J Exp Bot. 0:doi: 10.1093/jxb/erab254
   Natural variations in the P-type ATPase heavy metal transporter ZmHMA3 controlling cadmium accumulation in maize grains
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Madzima, TF; MacIntosh, G. 2021. Plant Cell. 0:doi: 10.1093/plcell/koab186
   Equity, diversity, and inclusion efforts in professional societies: intention vs. reaction

The authors discuss important developments in equity, diversity, and inclusion (EDI) efforts by academic institutions and professional societies, especially related to Plant Sciences. They discuss 'reflective assessments' of departments and professional societies to identify discrepancies by making a detailed analysis of community demographics that includes ranks and roles. The authors cite evidence that organizations do not naturally diversify, and provide concrete suggestions for "intensional inclusion" of under-represented groups. This paper is a thought provoking work that can help repair the current exclusionary climates in biology and especially in plant sciences. MaizeGDB team, 2021

Madzima, TF; MacIntosh, G. 2021. Plant Cell. 0:doi: 10.1093/plcell/koab186
   Equity, diversity, and inclusion efforts in professional societies: intention vs. reaction
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Jumper, J. 2021. Nature. 0:10.1038/s41586-021-03819-2
   Highly accurate protein structure prediction with AlphaFold

Game-Changing Development: Google DeepMind's AlphaFold 2 handily won the 14th Critical Assessment of Structural Prediction (CASP14) competition in Nov 2020, and the paper describing the AlphaFold 2 neural network masterpiece was published July 15, 2021. The authors state: "In this work, we develop the first computational approach capable of predicting protein structures to near experimental accuracy in a majority of cases. Indeed, AlphaFold 2 can predict protein structure as well as X-ray crystallography in many cases. Structural information of proteins is essential in biology, and AlphaFold 2 will have profound implications for medicine, technology, basic biology, gene annotation and much much more. DeepMind and EMBL-EBI have partnered to release the predicted protein structure of all sequences in UniProt. An initial release 22 species, including B73 RefGen_v4 and maize RefSeq genes, can be found here: https://alphafold.ebi.ac.uk. MaizeGDB, 2021

Jumper, J. 2021. Nature. 0:10.1038/s41586-021-03819-2
   Highly accurate protein structure prediction with AlphaFold
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McKenna, JF, et al. 2021. Frontiers Plant Sci. 12:645218
   Maize (Zea mays L.) nucleoskeletal proteins regulate nuclear envelope remodeling and function in stomatal complex development and pollen viability

Nuclear membrane proteins are important for relaying signal from cytoplasm to inside the nucleus and has major role in cellular mechanosensing. Despite their important role, it took long time to discover the maize nuclear membrane proteins, due to their lack of conservancy with other known nuclear membrane proteins. In recent years, Hank Bass' group has started to identify and characterize the role of maize LINC (Linker of Nucleoskeleton and Cytoskeleton) complex proteins. In a continuation to this process, McKenna et al. studied 3 proteins (NCH1, NCH2, and MKAKU41) from this complex to understand their cellular localization and functional role during plant development. From their cellular expression data, using tobacco leaf, they have demonstrated that these three proteins act like other known LINC complex associated proteins. Additionally, they have found that MKAKU41 is important for maintaining nuclear shape, stomatal development, and pollen viability. This study takes our understanding about the functional role of maize LINC complex proteins one step further. Arif Ashraf, 2021

Genes: NCH1 (Zm00001d051600), NCH2 (Zm00001d043335), MKAKU41 (Zm00001d026487)

McKenna, JF, et al. 2021. Frontiers Plant Sci. 12:645218
   Maize (Zea mays L.) nucleoskeletal proteins regulate nuclear envelope remodeling and function in stomatal complex development and pollen viability
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Song, BX, et al. 2021. Genome Res. 0:doi: 10.1101/gr.266528.120
   Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize

Conserved non-coding sequences (CNSs) are islands of non-coding sequence showing an unexpectedly low level of divergence between related species. Although the specific functions of CNSs remain unclear, many CNSs are likely to function as cis-regulatory elements involved in regulating gene transcription and chromatin structure. Song and his colleagues developed a sensitive sequence alignment pipeline, and identified CNSs in the Andropogoneae tribe, which contains many important crop species, such as maize, sorghum, sugarcane and silvergrass. They found that a large proportion (86%) of CNSs were located within 2 kb of genes and within genes including introns, UTRs, putative cis-regulatory elements, chromatin loop anchors, noncoding RNA genes, and several transposable element superfamilies. Further investigation indicated that these CNSs were enriched in active regions of DNA replication in the early S phase of the mitotic cell cycle and different groups of CNSs exhibited different DNA methylation ratios. Analysis of the CNS presence and absence within the 2-kb upstream region of a gene with the expression of the gene demonstrated that loss of CNSs was associated with loss of gene expression, suggesting the potential role of the CNSs in shaping the expression patterns of their flanking genes. Furthermore, they also compared CNS variation between the two maize subgenomes, and found that the dominant duplicated gene copy harbored an overall longer CNS. Together these data provide some new insights into understanding the roles of CNSs as regulatory elements in regulation of genes. Meixia Zhao 2021

Song, BX, et al. 2021. Genome Res. 0:doi: 10.1101/gr.266528.120
   Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
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Best, NB, et al. 2021. G3. 0:doi: 10.1093/g3journal/jkab106
   Mutation of the nuclear pore complex component, aladin1, disrupts asymmetric cell division in Zea mays (maize)

The nucleus is protected by dual membranes (inner and outer membrane) and most of the molecular transport happens through nuclear pore complex (NPC). In recent years, human, fungal, and algal NPC structures were revealed in much better resolution due to the advancement of cryo-EM. In contrast, plant NPC and its components are poorly understood. In this article, Best et al. identified two independent alleles, ali1-1 and ali1-2, of NPC component aladin1, which is conserved in other organisms as well. ali1-1 has G to A transition in exon 16 and ali1-2 has C to T transition in exon 10. In both alleles, it causes premature stop codon, and last 16 and 134 amino acids are missing for ali1-1 and ali1-2, respectively. Mutation of aladin1 demonstrates several phenotypes including plant stature, tassel architecture, and abnormal subsidiary cells. From the RNA-seq analysis, the authors demonstrated that other NPC components are up-regulated in ali1-1 mutants. Additionally, expression of polarized proteins required for stomatal development (PAN1 and BRICK1) are downregulated at transcriptional level, which corroborates with the abnormal asymmetric cell division of subsidiary mother cells (SMC). This study identified the role of one of the conserved NPC components, ALADIN1, in plant development and opened the door for asking more in-depth questions for its role in asymmetric cell division. Arif Ashraf, 2021

Zm00001d023264 = ALADIN1

Best, NB, et al. 2021. G3. 0:doi: 10.1093/g3journal/jkab106
   Mutation of the nuclear pore complex component, aladin1, disrupts asymmetric cell division in Zea mays (maize)
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Bezrutczyk, M, et al. 2021. Plant Cell. 0:doi: 10.1093/plcell/koaa055
   Evidence for phloem loading via the abaxial bundle sheath cells in maize leaves

Maize is referred to as C4 crop, which has a significantly higher productivity rate than many other crops. Different structures on the upper (adaxial) and lower (abaxial) sides of plant leaves performs different tasks. In maize, sucrose transporters (SWEET) act in the bundle sheath cells on the abaxial side of the leaf. Researchers wonders if different cell types from maize adaxial and abaxial side could answer what is the effective way for maize to distribute the photoassimilates produced during photosynthesis throughout the plant. Dr. Ji Yun Kim and its college used single cell sequencing approach to distinguish between different types of bundle sheath cells in a maize leaf, and identified abaxial bundle sheath cells as being specialized in nutrient transport. And in the abaxial bundle sheath cells, most of the sucrose transporters including SWEET13a, b, and c, and amino acid transporters were highly enriched. These suggests a phloem loading pathway via two abaxial bundle sheath cells which have large surface area, to transfer sucrose. Yanfang Du, 2021

SWEET13a: Zm00001d023677; SWEET13b, Zm00001d023673; SWEET13c: Zm00001d041067; Membrane H+ ATPase3, Zm00001d019062; AAP45, Zm00001d035243; AAP56, Zm00001d012231; STP3, Zm00001d027268.

Bezrutczyk, M, et al. 2021. Plant Cell. 0:doi: 10.1093/plcell/koaa055
   Evidence for phloem loading via the abaxial bundle sheath cells in maize leaves
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Chen, ZL, et al. 2021. Nature communications. 12:2378
   Structural variation at the maize WUSCHEL1 locus alters stem cell organization in inflorescences

Genes: ZmWUS1 (GRMZM2G047448); ZmLOG7a (GRMZM2G059392); ZmLOG7c (GRMZM5G842645); ZmIAA9 (GRMZM2G057067); ZmOCL4(GRMZM2G123140);ZmCLE7 (GRMZM2G372364); KN1 (GRMZM2G017087); ZYB15 (GRMZM2G529859)

RNA-seq datasets are deposited in GEO with accession code GSE158330. Genomic sequences of ZmWUS1-A and ZmWUS1-B loci in the Bif3 mutant are available in GenBank (accession numbers MW677561, MW677562, MW677563)

Plant meristem contains a small group of stem cells at the apical domain, and the population size of these stem cells is controlled by the CLAVATA-WUSCHEL (CLV-WUS) negative feedback-loop through regulating the expression of the WUS. The maize genome encodes two WUS orthologs, ZmWUS1 and ZmWUS2, however, the functional counterparts of WUS are still tricky in maize. In this study, Chen and his colleges found a novel maize dominant Barren inflorescence3 (Bif3) mutant, which harbors a tandem duplicated copy of the ZmWUS1 gene, ZmWUS1-B, whose novel promoter enhances transcription in a ring-like pattern. The multimerized binding sites in the promoter region of ZmWUS1-B containing the cytokinin (CK) signaling-related cis-acting element that can be bound by cytokinin signaling type-B RESPONSE REGULATORs (RRs), and thus leading to the overexpression of ZmWUS1-B and increase the sensitivity to cytokinin. Hypersensitivity to cytokinin causes stem cell over-proliferation and major rearrangements of Bif3 inflorescence meristems, leading to the formation of ball-shaped ears with less branches and severely affecting productivity. These findings place ZmWUS1 at the center of the gene-regulatory networks of meristem size, thus enhancing our ability to exploit variation in the CLV-WUS pathway for diverse agricultural traits, and highlight the striking effect of cis-regulatory variation on a key developmental program. Yanfang Du, 2021

Chen, ZL, et al. 2021. Nature communications. 12:2378
   Structural variation at the maize WUSCHEL1 locus alters stem cell organization in inflorescences
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Chatterjee, D, et al. 2021. Plant Physiol. 0:doi: 10.1093/plphys/kiab183
   Maize unstable factor for orange1 is essential for endosperm development and carbohydrate accumulation

In this study, Chatterjee et al. characterized dominant mutation of unstable factor for oragnge1 (ufo1) gene. Multiple alleles of ufo1 (ufo1-1 (U-E), ufo1-1 (U-S), and ufo1-Dsg) indicate its role in seed weight and carbohydrate accumulation. Further experiment suggests that ufo1-1 (U-E) and ufo1-Dsg have defects in basal endosperm cell differentiation. Furthermore, mutation of ufo1 leads to the alteration of endogenous phytohormone concentration during seed development. Overexpression of ufo1 regulates the expression of genes known for endosperm development. Authors have further validated a set of differentially expressed genes by crossing U-E allele with FL2-RFP, GLB3-RFP, and RAB17-YFP. Among these three transgenic lines, FL2-RFP and GLB3-RFP are known as seed storage proteins and RAB17-YFP for ABA responsive gene. All these three transgenic lines demonstrated reduced fluorescence signals in the U-E allele background compared to control, except increased fluorescence of RAB17-YFP in the pedicel in U-E background. Altogether, this article highlights the role of Ufo1 gene in multiple developmental processes, including seed development. Arif Ashraf, 2021

Genes: ufo1 GRMZM2G053177 (Zm00001d000009)

GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117782

Chatterjee, D, et al. 2021. Plant Physiol. 0:doi: 10.1093/plphys/kiab183
   Maize unstable factor for orange1 is essential for endosperm development and carbohydrate accumulation
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Liang, XY, et al. 2021. New Phytol. 0:doi: 10.1111/nph.17323
   Metabolomics-driven gene mining and genetic improvement of tolerance to salt-induced osmotic stress in maize

The natural maize varieties have been known to have a large diversity of salt tolerance, and a couple of loci have been identified the salinity tolerance functions recently, the genetic mechanism underlying the complexity of the salt-induced osmotic stress (SIOS), however, still requires further work. Caifu Jiang and his colleges performed a comprehensive metabolite profiling of 266 maize inbred lines, which were randomly selected from a larger GWAS population. Through non-targeted liquid chromatography-mass spectrometry (LC-MS)-based metabolomics as well as computational clustering, they compared the metabolomes under control and salt conditions, and identified 37 metabolite biomarkers of SIOS tolerance. By metabolic GWAS (mGWAS) strategy, SNPs significantly associated with the above-mentioned metabolite markers were identified. Three out of the corresponding candidate genes were selected for validation by CRISPR/Cas9 knockout or overexpression. Finally, Favorable alleles were then introgressed into elite maize inbred lines, and the resulting near-isogenic lines show a nice effect on salt tolerance improvement. This stunning study demonstrates the strategy of combing metabolomics and natural variance in maize, and similar approaches can be generally employed to understand the metabolic aspects underpinning other complex crop traits. Zhaobin Dong, 2021

Liang, XY, et al. 2021. New Phytol. 0:doi: 10.1111/nph.17323
   Metabolomics-driven gene mining and genetic improvement of tolerance to salt-induced osmotic stress in maize
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Swarts, KL et al. 2021. Heredity pp.doi: 10.1038/s41437-021-00422-z
   Joint analysis of days to flowering reveals independent temperate adaptations in maize

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Swarts, KL et al. 2021. Heredity pp.doi: 10.1038/s41437-021-00422-z
   Joint analysis of days to flowering reveals independent temperate adaptations in maize
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Marand, AP; Chen, ZL; Gallavotti, A; Schmitz, RJ. 2021. Cell. 0:doi: 10.1016/j.cell.2021.04.014
   A cis-regulatory atlas in maize at single-cell resolution

genes charaterized: IDP1439, IDP322, IDP8357, IDP844, aaap21, aaap52, aaap54, aaap64, ad1, ago18b, agp2, aic1, apt1, arftf29, arftf3, arftf4, asg42, ba1, ba2, baf1, bd1, bde1, bhlh10, bhlh130, bhlh139, bhlh175, bhlh19, bhlh22, bhlh24, bhlh43, bhlh82, bhlh96, bif1, bif2, bif4, bk2, bk4, bm5, brk3, cah1, ccp5, cl218_1, cncr1, dct2, drl2, epf1, epf2, ereb206, ereb4, ereb53, fcp1, fdl1, fea3, fea4, gif1, glk53, gpat11, gpat12, gras19, gras37, gras58, gras85, grp4, gt1, hb124, hb67, hb75, hb8, ifa1, ig1, irx15, kch1, kch3, kch4, kcs1, kn1, lbd1, lbd24, limtf13, lox4, lrp1, lsi2, mab1, mdh6, me3, miR166a, mpkl1, myb1, myb105, myb7, na1, nactf103, nactf116, nactf131, nactf36, nactf57, nactf77, nactf78, nactf92, nc1, ns1, ns2, obf1, obf4, ocl1, ocl2, ocl3, ocl4, ocl5a, ork1, oxmt1, pan2, pdrp1, pep1, pin1, pin2, pin3, pin9, pmm1, pve1, pza03344, r1, ra1, ra2, ra3, rcp1, rcph2, rel2, rld1, rop2, rop9, rs1, rtcl1, rtcs1, rte1, rte2, rth6, rum1, scro1, si1, sid1, sk1, slac1, spi1, spms1, ssu1, ssu2, su2, sut1, sut2, sut3, sut4, sut5, sut6, sut7, sweet13b, sweet14b, sweet1b, tb1, te1, tga1, tmm1, tru1, ts2, ts6, tsh1, tsh4, tt1, ub2, ub3, ufg25, ugu1, umc126a, vt2, wox4, wox5b, wrky64, wx1, yab14, yab15, yab9, zag1, zag2, zap1, zll3, zmm16, zmm18, zmm2, zmm29, zmm8

The authors analyses can be readily reproduced by leveraging the freely available code implemented throughout the study (https://github.com/plantformatics/maize_single_cell_cis_regulatory_atlas). Researchers analyzing scATAC-seq data can benefit from extensive documentation and tutorials accompanying our R package, Socrates (https://github.com/plantformatics/Socrates).

Genome Browser B73_v4 with data from this paper: http://epigenome. genetics.uga.edu/PlantEpigenome/index.html

Cis-regulatory elements (CREs), which can regulate spatiotemporal gene expression, are prevalent in plants, especially in species with large genomes, such as maize. To comprehensively assess cis-regulatory variation among different cell types in maize, Marand and his colleagues used single-cell genomics in 72,090 nuclei across six maize organs, and constructed the first cis-regulatory atlas at a single cell level. They determined cis- and trans-regulatory factors underlying cell identities using single-cell sequencing of assay for transposase accessible chromatin to reveal transcription factors (TFs) coordinating chromatin interactions, to identify TFs with non-cell-autonomous activity, and to implicate CREs with enhancer activity and interactive capacity as substantial sources of trait variation. In addition, they also uncovered that unmethylated long terminal repeat retrotransposons are a significant source of cis-regulatory variation and played a central role in shaping regulatory circuitries across evolutionary timescales. Furthermore, their research identified cell-type-specific CREs that are associated with agronomic traits under domestication during modern maize breeding, suggesting the importance of these CREs. Finally, they present the R package, Socrates, a unified framework for scATAC-seq preprocessing, normalization, and downstream analysis. This single-cell cis-regulatory atlas would be a valuable resource for the entire maize community, and the bioinformatics software is very useful to understand cis-regulatory variation in any species. This research would make excellent contributions to several research areas including epigenomics, gene regulation, genome evolution and many others. Meixia Zhao, 2021

Marand, AP; Chen, ZL; Gallavotti, A; Schmitz, RJ. 2021. Cell. 0:doi: 10.1016/j.cell.2021.04.014
   A cis-regulatory atlas in maize at single-cell resolution
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Yu, P, et al. 2021. Nature Plants. 0:doi: 10.1038/s41477-021-00897-y
   Plant flavones enrich rhizosphere Oxalobacteraceae to improve maize performance under nitrogen deprivation

Yu et al. took the different sections of root (0.5-2, 2-4, and 4-7 cm zone) from 20 inbred lines to understand the role of differentially expressed genes in developmental context and as well as plant-microbe interaction. They found the bacterial community associated with the different sections of roots in all the inbred lines. Among these inbred lines, 787 performs better and is associated with a unique bacterial community. It has been found that 787 secretes significantly higher amounts of flavonoids (apigenin and luteolin) compared to poorly performing inbred lines such as LH93. If LH93 is transferred to 787-growing soil, then LH93 performs better, which clearly suggests the role of the unique bacterial community associated with 787. Furthermore, using flavonoid biosynthetic pathway mutant C2-idf, it has been demonstrated that absence of flavonoids fails to attract specific microbial communities and is less efficient in nitrogen fixation. Authors have tested the growth performance of several root defective mutants (lrt1, rum1, rth6, rtcs) using flavonoid-conditioned rhizosphere microbiota. They have found that lrt1 mutant has increased the number of emerging lateral root density when transplanted in the 787-grown soil. Together, the story suggests a model where flavonoid-mediated enrichment of microbial community to fix more nitrogen and better plant growth by inducing lateral root formation in lrt1 mutant. Arif Ashraf, 2021

All raw plant RNA-seq data, rhizosphere bacterial 16S and fungal ITS and shotgun metagenomic sequencing data reported in this paper were deposited in the Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) under accession no. SRP263360. RNA-seq reads were mapped to the maize reference genome sequence v.4 (https://www.maizegdb.org/genome/genome_assembly/Zm-B73-REFERENCE-GRAMENE-4.0). The SSUrRNA database from SILVA database (release 128, 2016, https://www.arb-silva.de/) and UNITE database (v.7.2, 2017, https://unite.ut.ee/) were used for analysis of bacterial 16S and fungal ITS sequences, respectively. The databases AgriGO (v.2.0, 2017, http://systemsbiology. cau.edu.cn/agriGOv2/) and REVIGO (2017, http://revigo.irb.hr/) were used for functional GO analysis of maize genes. Protein-protein interaction networks of enriched gene modules were generated by the database STRING (v.10.5, https://version-10-5.string-db.org/). Functional annotation of shotgun metagenomic sequencing was performed using COG databases (release clovr-1.0-RC9). We deposited customized scripts on the association of gene modules with microbial taxonomic traits in the following GitHub repository: https://github.com/PengYuMaize/Yu2021NaturePlants. Source data are provided with this paper.

Yu, P, et al. 2021. Nature Plants. 0:doi: 10.1038/s41477-021-00897-y
   Plant flavones enrich rhizosphere Oxalobacteraceae to improve maize performance under nitrogen deprivation
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McCaw, ME, et al. 2020. Frontiers in Genome Editing. 2:DOI=10.3389/fgeed.2020.622227
   Development of a transformable fast-flowering mini-maize as a tool for maize gene editing

Fast-Flowering Mini-Maize (FFMM) lines A and B were recently developed as a useful tool for maize research by reducing the generation time and the space required. Both lines can go from seed-to-seed in 60 days and produce 5-6 generations per year. However, neither line was able to be successfully utilized for transformation via standard methods. The authors successfully created a line of FFMM via inbreeding and double haploid methods, by hybridizing Hi-II A, a transformable maize genotype, with FFMM-A. This new line, FFMM-AT, have the ability to form callus and be transformed via a standard Agrobacterium mediated method for mutagenesis via a CRISPR-Cas9 system. The transformation frequencies of transgenic event producing T1 seeds per 100 infected embryos ranged from 0 -17.1% and approximately 80% of transgenic plants analyzed showed mutations at the target sites. This new line, FFMM-AT, can serve as a useful open-source resource for the maize community. Brianna Griffin, 2021

Published in Frontiers in Genomic Editing https://www.frontiersin.org/articles/10.3389/fgeed.2020.622227/full

McCaw, ME, et al. 2020. Frontiers in Genome Editing. 2:DOI=10.3389/fgeed.2020.622227
   Development of a transformable fast-flowering mini-maize as a tool for maize gene editing
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Long, J-C et al. 2021. Plant Cell 33:2183-2196
   Maize decrease in DNA methylation 1 targets RNA-directed DNA methylation on active chromatin

DNA methylation is an important mechanism to suppress the activity of transposable elements (TEs), which comprise a large proportion of the maize genome. Silencing of TEs can be initially triggered by 24 nt small interfering RNAs (siRNAs) and maintained by different epigenetic pathways including several components, such as the chromatin-remodeling factor Decrease in DNA methylation 1 (DDM1). There is evidence that DDM1 is involved in the maintenance of DNA methylation, but the role of DDM1 in RNA directed DNA methylation (RdDM) remains unclear. Long and his colleagues performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) in developing maize embryos to investigate the genome-wide occupancy of DDM1 in the maize genome. Their research detected an 8-bp GC-rich degenerate DNA sequence motif "GCYGCYGC" that is recognized by ZmDDM1. This motif is largely enriched in transcription stat sites (TSSs) and other intergenic regions, and seems to be associated with gene transcriptional state. In addition, they also found that ZmDDM1-occupied genes exhibited a large abundant 24 nt siRNAs and much higher levels of CHH (H = A, T, or C) methylation. Furthermore, the ZmDDM1-binding sites in the intergenic regions are associated with active chromatin, such as H3K4me3 and H3K9ac, and exhibited low levels of suppressed epigenetic marks, such as H3K9me2, CG and CHG methylation. Given that 24 nt siRNAs are loaded into ARGONAUTE4 (AGO4) protein, they also found that ZmDDM1-target regions largely overlapped with ZmAGO4-bound genomic sites, suggesting that ZmDDM1 may work together with ZmAGO4 in the process of RdDM in maize. This research dissects the novel role of ZmDDM1 in RdDM in maize. Meixia Zhao, 2021

All sequence data are available at the National Center for Biotechnology Information Sequence Read Archive under accession number GSE162678.

Long, J-C et al. 2021. Plant Cell 33:2183-2196
   Maize decrease in DNA methylation 1 targets RNA-directed DNA methylation on active chromatin
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McLean-Rodriguez, FD; Costich, DE; Camacho-Villa, TC; Pe, ME; Dell'Acqua, M. 2021. Heredity. 0:doi: 10.1038/s41437-021-00423-y
   Genetic diversity and selection signatures in maize landraces compared across 50 years of in situ and ex situ conservation

McLean-Rodriguez et al (2021) compare the genetic diversity of 13 paired samples. These seed lots have been kept in either ex situ conservation (sampled in 1967 by CIMMYT) or in situ conservation (maintained and used in farmer fields) for the last 50 years. Using a set of ~74,000 SNPs, they found heterozygosity was similar between in situ and ex situ samples. Allelic diversity was slightly lower in the in situ samples, but this was driven by 3 of the 13 accessions. Fst was smaller between in situ accessions, suggesting potential gene flow between landraces. There was little evidence of genetic drift in the ex situ accessions, likely because these have only been regenerated twice. Additionally there was little population structure, with the limited structure related to altitudinal gradients and the chromosomal region of the inv4m polymorphism, a known adaptive variant to highland conditions. Taken altogether, ex situ accessions are representative of the genetic diversity still present in farmer's fields. Additionally, selective scans indicate 8-10 potential outlier regions that are likely in response to farmer selection on ear and kernel traits, indicating current evolution within farmer fields. This study showcases the potential of including farmers in research and conservation efforts. Samantha Snodgrass, 2021

All raw reads are deposited at the European Nucleotide Archive (https://www.ebi.ac.uk/=) under study PRJEB41410. Allele calls used in the study are available in VCF format at https://doi.org/10.6084/m9.figshare.13199918. R scripts used for the analyses are stored on the GitHub page of the corresponding author at https://github.com/mdellh2o/morelosMAIZE.

McLean-Rodriguez, FD; Costich, DE; Camacho-Villa, TC; Pe, ME; Dell'Acqua, M. 2021. Heredity. 0:doi: 10.1038/s41437-021-00423-y
   Genetic diversity and selection signatures in maize landraces compared across 50 years of in situ and ex situ conservation
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Liu, BX, et al. 2021. Plant Cell. 0:doi: 10.1093/plcell/koab083
   Manipulating ZmEXPA4 expression ameliorates the drought-induced prolonged anthesis and silking interval in maize

Coordinated shedding from the tassel and silking in the ear is essential for maize pollination. Drought at the flowering time, however, usually harasses the synchronous development of the tassel and ear, resulting in extended anthesis and silking interval (ASI). To investigate how the maize reproductive tissue responds to the drought, Liu et al performed a detailed comparison and found that the effect of drought on the development of ears is more evident than that of the tassels. Then a comprehensive drought transcriptome atlas of maize ears was performed, and genes involved in cell expansion and growth were repressed by drought as expected. However, the developmental and floral organ identity genes were rarely affected by drought, which is a bit surprising. The function of one expansin gene ZmEXPA4 for ASI and drought response was recapitulated by candidate gene associated analysis, followed by genetic engineering on the gene to confirm its drought-induced expression correlating with the reduced ASI. This study provided new insights into the molecular mechanism of drought stress leading to the increase of ASI in maize, and proposed a promising blueprint for improving ASI traits. Zhaobin Dong, 2021

ZmEXPA4 = Zm00001d034663

Sequence data from this article can be found in the GenBank libraries under the following accession number: ZmEXPA4:ONM10950.1. Additional accession numbers are listed in Supplemental Data Sets S1 and S2. The RNA-seq data from this article can be found in the Genome Sequence Archive under accession number PRJNA659061.

Liu, BX, et al. 2021. Plant Cell. 0:doi: 10.1093/plcell/koab083
   Manipulating ZmEXPA4 expression ameliorates the drought-induced prolonged anthesis and silking interval in maize
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Du, YF, et al. 2021. Proc Natl Acad Sci, USA. 118:e2019218118
   Gene duplication at the Fascicled ear1 locus controls the fate of inflorescence meristem cells in maize

Du et al (2021) dissect the Fascicled ear1 (Fas1) locus. Fas1 mutants have deeply branching male and female inflorescences, and Du and colleagues used scanning electron microscopy to trace this to an enlargement of the peripheral zone of the inflorescence meristem (IM) and shrinkage of the central zone. They mapped the Fas1 locus to ~160Kbp on chromosome 9 that captures two genes in B73, zmm8 and drl2. Fas1 mutants show evidence of multiple copies of these two genes, and interestingly, so do the inbred lines B97 and Oh43, even though these inbred lines do not have the same Fas1 phenotypes. 5' Rapid Amplification of cDNA Ends (RACE) found transcripts with 5'-UTRs specific to the Fas1 mutants compared to other lines. Yeast two-hybrid assays demonstrate that zmm8 and drl2can interact. Expression of these genes normally do not overlap, but they do in the Fas1 mutants. Additionally, Fas1 mutants upregulate known genes that promote the peripheral zone of the IM while suppressing genes that promote the central zone. Taken all together, the authors propose tandem duplications and rearrangements of this region in the Fas1 mutants has created novel enhancer and/or promoter regions resulting in the misexpression of zmm8 and drl2 to be earlier in IM development, resulting in deeply branched inflorescences. Samantha Snodgrass, 2021

RNA-seq data are deposted at NCBI (National Center for Biology Information), accession number: PRJNA698219.

Genes characterized: zmm8 Zm00001d048082 drl2 Zm00001d048083

Du, YF, et al. 2021. Proc Natl Acad Sci, USA. 118:e2019218118
   Gene duplication at the Fascicled ear1 locus controls the fate of inflorescence meristem cells in maize
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Liu, L, et al. 2021. Nature Plants. 0:doi: 10.1038/s41477-021-00858-5
   Enhancing grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes

CRISPR/Cas9 genome editing of promoters generates diverse cis regulatory alleles that provide beneficial quantitative variation for breeding. Meristem size, which is controlled by CLE peptide signals in the CLAVATA WUSCHEL feedback loop, is one of the strategy to improve crop grain yield by increasing seed number. However, the strong alleles with mutations in CLV genes cause meristem over-proliferation, leading to enlarged inflorescence stems and fasciated ears in maize that develop many more disorganized and shorter kernel rows with low grain yield. Interestingly, weak alleles maintain meristem organization and ear length, highlighting the potential to quantitatively manipulate fea genes for yield enhancement, like weak coding sequence alleles of fasciated ear2 (fea2) and fea3. In this study, Liu and his colleges engineered quantitative variation for yield-related traits in maize by making weak promoter alleles of two CLE genes, ZmCLE7 and ZmFCP1, with nine single-guide RNAs (sgRNAs) targeting promoter regions of roughly 2 kilobases (kb) for ZmCLE7 and roughly 1.1 kb for ZmFCP1, using CRISPR-Cas9 genome editing. Detecting the genes expression level and the evaluating the yield-related traits, their results indicate that proximal promoter engineering can also modify traits quantitatively to enhance crop yields, and distal cis-regulatory variation largely reshaped plant and inflorescence morphology during maize domestication and improvement, as well as that in tomato. Yanfang Du, 2021

ZmCLE7: GRMZM2G372364, ZmFCP1: GRMZM2G165836.

Liu, L, et al. 2021. Nature Plants. 0:doi: 10.1038/s41477-021-00858-5
   Enhancing grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes
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Liang, ZK, et al. 2021. Plant Physiol. 0:doi: 10.1093/plphys/kiab073
   Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize

Although transposable elements (TEs) are ubiquitous in most eukaryotic species, most of them are largely silenced by epigenetic pathways. However, silencing of TEs can be alleviated in response to different environments. Liang and his colleagues investigated the expression of TEs in three maize inbred lines (B73, W22 and Mo17) in response to heat and cold stresses. They find that overall a substantial number of TE families respond to abiotic stress, but the majority of TE families do not exhibit changes in expression level in these stress conditions. When they zoomed in on a subset of TE families, their data show that the stress-responsive activation of a TE family is likely caused by a small number of elements in the family where DNA methylation is absent. Furthermore, the same TEs without DNA methylation in one genotype is more likely to be activated than those with high DNA methylation levels in other genotypes. Their data suggest that the activation of TEs is largely dependent on their chromatin states, such as DNA methylation, in response to stress conditions. This genome wide analysis lines well with published research that being exposure to hypomethylation of TEs can speed up the reactivation of them. This study sheds new lights on the regulation of expression of TEs in normal and stress conditions and demonstrates the important roles of epigenetic marks in controlling TE silencing. Meixia Zhao, 2021

Liang, ZK, et al. 2021. Plant Physiol. 0:doi: 10.1093/plphys/kiab073
   Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize
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Blein-Nicolas, M, et al. 2020. Genome Res. 0:doi: 10.1101/gr.255224.119
   A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize

Drought remains a major global maize devastator. Drought response mechanisms remains a very complex field of study resulting in molecular responses involving signaling molecules, hormones, metabolite accumulation, drought response protein accumulation, as well as various physiological responses. These changes are also highly dependent on environmental factors. All of this taken together results in very complex system to study. The authors goal was to elucidate the genotype-phenotype relationship related to drought tolerance in maize. They used a systems biology approach that combined mass spectrometry-based proteomics data acquired from 254 maize genotypes and integrated this with GWAS, coexpression networks and ecophysiological phenotype data using correlation analysis and QTL/pQTL colocalizations. The authors found that even mild drought can cause dramatic changes in the proteome including in proteins related to stress response. In addition, they identified different candidate genes that are potentially responsible for coexpression of stress-response proteins and the variation of drought response phenotypes. This is significant because it provides new understanding of the molecular mechanisms of drought resistance. Brianna Griffin, 2021

Blein-Nicolas, M, et al. 2020. Genome Res. 0:doi: 10.1101/gr.255224.119
   A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize
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Kong, DX, et al. 2021. New Phytol. 0:doi: 10.1111/nph.17293
   ZmSPL10/14/26 are required for epidermal hair cell fate specification on maize leaf

In this study, Kong et al. identified three transcription factors (TFs), ZmSPL10, ZmSPL14, and ZmSPL26, required for regulating epidermal hair cell fate specification in the maize leaf. These three TFs have detectable expression in the leaf base during development (except ZmSPL26) and localize in the nucleus. CRISPR-Cas9-edited triple knockout mutant, Zmspl10/14/26, has hairless glabrous leaf phenotype. Additionally, the expression of ZmWOX3A is reduced in the triple knockout mutant. Further analysis based on Y1H and EMSA demonstrated that ZmSPL10/14/26 directly binds to the promoter region of ZmWOX3A. Apart from regulating ZmWOX3A, several auxin-related genes (ZmYUC2, ZmPIN1b, ZmPIN1c, ZmARF18) are regulated by these three TFs. Altogether, this work highlighted ZmSPL10/14/26-mediated hair cell specification through ZmWOX3A and auxin-dependent manner. Arif Ashraf, 2021

ZmSPL10 (Zm00001d015451), ZmSPL14 (Zm00001d036692) ZmSPL26 (Zm00001d053756)

Kong, DX, et al. 2021. New Phytol. 0:doi: 10.1111/nph.17293
   ZmSPL10/14/26 are required for epidermal hair cell fate specification on maize leaf
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Liang, YM; Liu, HJ; Yan, JB; Tian, F. pp. 10.1146/annurev-arplant-080720-090632
   Natural Variation in Crops: Realized Understanding, Continuing Promise

Natural alleles are ideal experimental disturbances for characterizing causal genotype-phenotype connections and the corresponding molecular mechanisms for millions of years. During the last three decades, natural variants of many genes corresponding to various important traits have been cloned, providing fundamental resources for knowledge guided crop domestication and improvement. In this review, the author summarized the genetic analysis of natural mutations and QTLs cloning strategies, and compared the advantages and disadvantages of various genetic mapping methods. Importantly, through the comprehensive analysis of 364 QTLs in six crops, including rice and maize, they provide a picture of the molecular, regulatory, and evolutionary mechanisms of natural variation. The author concluded that transcription factors play important roles in domestication and adaptation regulation; Enzymes encoding genes are more important in the regulation of yield and quality-related traits; Biological and abiotic stress traits are controlled by genes and belong to various categories. Interestingly, in hybrid maize, QTLs are almost located in the regulatory region, while in self-bred crops, the QTLs of rice, wheat, barley and soybean mainly exist in the gene coding region. They also predicted the potential advantages of genome-editing techniques in crop improvement breeding by creating de novo alleles, pyramiding favorable alleles from multiple genes, designing novel sequences for enhancing traits, or even generating new traits, which provides a powerful strategy for responding to the demand for food caused by population growth and environmental changes. Yanfang Du, 2021

Liang, YM; Liu, HJ; Yan, JB; Tian, F. pp. 10.1146/annurev-arplant-080720-090632
   Natural Variation in Crops: Realized Understanding, Continuing Promise
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Zhao, M, et al. 2021. Proc Natl Acad Sci, USA. 118:e2009475118
   The mop1 mutation affects the recombination landscape in maize

Meiotic recombination generates genetic diversity and ensures the accurate segregation of homologous chromosomes. However, the role of chromatin in recombination remains poorly understood. Zhao and her colleagues examined the effects on meiotic recombination of a mutation in a component of the RNA-directed DNA methylation (RdDM) pathway, MOP1 (mediator of paramutation1), a putative RNA-dependent RNA polymerase, as well as a mutation in a component of the trans-acting small interference RNA biogenesis pathway, Lbl1(Leafbladeless1) in maize. They found that in mop1 mutants, meiotic recombination was uniformly decreased in deeply silenced pericentromeric regions but was generally increased in gene rich chromosomal arms. Cytogenetic analysis further confirmed that overall meiotic crossovers (COs) are unchanged but occur more frequently in chromosomal arms. They proposed that the redistribution of meiotic recombination in mop1 mutants is caused by CO interference and constant CO numbers. Loss of CHH (where H = A, T, or C) methylation within regions near transcriptionally active genes in mop1 may be sufficient to trigger the changes in chromosomal arms that allow enhanced meiotic recombination but not sufficient to trigger these changes in heterochromatin. In addition, early CO in chromosomal arms may prevent CO formation in pericentromeric regions due to CO interference. Interestingly, the authors did not observe significant changes with respect to meiotic recombination frequency in lbl1 mutants. This research is the first report showing the impact of CHH methylation despite its low frequency on recombination in a large plant species with highly methylated genome, and sheds light on the role of epigenetic factors in meiotic recombination. Meixia Zhao, 2021

Zhao, M, et al. 2021. Proc Natl Acad Sci, USA. 118:e2009475118
   The mop1 mutation affects the recombination landscape in maize
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Vendramin, S; Huang, J; Crisp, PA; Madzima, TF; McGinnis, K. 2020. G3. 0:doi: 10.1016/j.cub.2018.05.072.
   Epigenetic regulation of ABA-induced transcriptional responses in maize

Vendramin and colleagues (2020) compared the transcriptional responses of wild type and mutant MOP1 maize seedlings under abscisic acid (ABA) treatment. ABA treatment induces abiotic stress responses while MOP1 is a known epigenetic regulator in the RNA-dependent DNA methylation (RdDM) pathway. The loss of MOP1 results in reduced DNA methylation, especially at CHH sites. Their analysis works to untangle the interactions between epigenetic and abiotic stress responses. Previously published gene expression changes to either ABA or mop1-1 were confirmed, but interestingly mop1-1 mutants showed magnified changes in gene expression under ABA-treatment. Vendramin and colleagues applied an Arabidopsis hierarchical transcription factor ABA response network to its maize orthologs. They found similar relationships and connectivity between the orthologs and target genes, suggesting a similar network at play in maize. Additionally, wildtype MOP1 seedlings had ABA-dependent CHH methylation, some of which targeted particular TE families, suggesting MOP1 mediated epigenetic changes may be important for environmental stress response. In sum, the different ABA responses in mop1-1 seedlings compared to wildtype could be due to disruption of hierarchical regulatory networks with cascading effects on transcription, MOP1-dependent ABA responses, and/or non-additive effects from the combined action of MOP1 and ABA response pathways. This work points to the potential importance of epigenetic regulation in maize stress responses. Samantha Snodgrass, 2021

Vendramin, S; Huang, J; Crisp, PA; Madzima, TF; McGinnis, K. 2020. G3. 0:doi: 10.1016/j.cub.2018.05.072.
   Epigenetic regulation of ABA-induced transcriptional responses in maize
Read More..

Yi, F, et al. 2020. Plant Physiol. 0:doi: 10.1093/plphys/kiaa060
   Miniature seed6, encoding an endoplasmic reticulum signal peptidase, is critical in seed development

This paper links mn6 to gene model GRMZM2G035526

Yi et al. characterized an endoplasmic reticulum(ER) signal peptidase and its specific function in kernel development. The authors isolated a new miniature seed mutant mn6, which showed a specific phenotype of reduced endosperm size due to defective seed filling. mn6 encodes an S26-family ER signal peptidase, and members of this family are critically involved in the protein secretion pathway by cleaving signal peptides. Expression analysis indicated Mn6 enriched in the developing kernels, consistent with the kernel specific phenotype of the mutant. There are two mn6 close paralogs (ZmSigP2 and ZmSigP3) in the maize B73 genome, but their expression level is much lower compared to that of mn6. In addition, CRISPR/CAS9 generated ZmSigP2 and ZmSigP3 mutants didn't show evident phenotype on the plant development, suggesting the predominant role of mn6 than other S26 family ER SPase members. The authors deployed mass spectrometric and immunoprecipitation analyses to identify the substrates of Mn6. They found Mn6 is putatively involved in the post-translational modification of carbohydrate synthesis-related proteins, including miniature seed1 (mn1), which is a cell wall invertase and specifically expressed in the basal endosperm transfer layer. Mn1 was much lower at both RNA and protein level in the mn6 background, which led to a significant reduction in cell wall invertase activity in the transfer layer, and consequently caused dramatic defects in endosperm filling. In conclusion, this study reveals the regulatory module between signal peptidase mn6 and its putative substrate mn1, proposing a promising possibility to modulate the MN6 activity for ideal endosperm filling in seed development. mn6 (GRMZM2G035526), mn1 (GRMZM2G119689), ZmSigP2 (GRMZM2G067080), ZmSigP3 (GRMZM2G307088). Zhaobin Dong, 2021

Yi, F, et al. 2020. Plant Physiol. 0:doi: 10.1093/plphys/kiaa060
   Miniature seed6, encoding an endoplasmic reticulum signal peptidase, is critical in seed development
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Xiang, Y et al. 2020. J Exp Bot 72:eraa507
   The transcription factor ZmNAC49 reduces stomatal density and improves drought tolerance in maize

NAC (NAM, ATAF, CUC) is a large group transcription factor and involved in plant development and abiotic stress responses as well. Xiang et al. characterize the role of one of the NAC transcription factors, ZmNAC49, for its involvement in drought response in maize. They have identified the expression of ZmNAC49 in different tissues, where it is most prominent in stem and leaf. Additionally, simulated drought stress induces the expression of ZmNAC49. Based on the drought-induced enhanced expression data, authors overexpressed the ZmNAC49 and observed drought resistance in the young transgenic maize plants. They further investigated ZmNAC49-mediated drought tolerance and identified reduced transpiration rate and stomatal conductance from their physiological experiments. This physiological data is also supported by the reduced stomatal density in these overexpression lines. In addition to their physiological evidence, molecular study suggests that ZmNAC49 regulates expression of stomatal developmental genes such as ZmTMM, ZmSDD1, ZmMUTE, and ZmFAMA. Among these genes, ZmNAC49 binds directly to the promoter region of ZmMUTE and reduces its expression. And ZmNAC49-mediated reduction of ZmMUTE expression is persistent even under drought stress. This study provided a comprehensive mechanistic pathway for ZmNAC49-mediated drought response in maize. Arif Ashraf, 2021

Genes: ZmNAC49 (GRMZM2G347043); ZmSTOMAGEN (NM_001149748.1); ZmTMM (NM_001137930.2); ZmSDD1 (NM_001137303.2); ZmSPCH (XM_008661417.2); ZmMUTE (XM_008657899.2); and ZmFAMA (XM_008657864.3).

Xiang, Y et al. 2020. J Exp Bot 72:eraa507
   The transcription factor ZmNAC49 reduces stomatal density and improves drought tolerance in maize
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Cruz, DF, et al. 2020. 16:e9667
   Using single-plant-omics in the field to link maize genes to functions and phenotypes

Lab controlled experiments studying genotype-phenotype have certain limitations including that their growth conditions do not reflect field conditions, and therefore are often of limited predicative value for field phenotype. Additionally, previous studies have found that combining multi-omics data (i.e.: transcriptomics and metabolomics) has stronger predictive value rather than using only one datatype. The authors propose a new strategy for a multi-omics technique to study molecular pathways and traits in the field and gain phenotypic data. The authors profiled the leaf transcriptome and metabolome, and different phenotypes for individual field grown B104 maize. Collected data was used to predict gene function and individual plant phenotype. The authors found that they could predict gene function and certain quantitative phenotypes. In particular, leaf and embryo phenotypes could be predicted at high rates, and overall, the authors made 1,334,456 novel gene predictions. This is significant because this method of field profiling can lead to new information about gene function and phenotype that can complement lab experiments, and more specifically may be very useful when profiling stress tolerance or yield improvement. Brianna Griffin, 2021

Cruz, DF, et al. 2020. 16:e9667
   Using single-plant-omics in the field to link maize genes to functions and phenotypes
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Dang, MQ et al. 2020. Int J Mol Sci 21:35
   Proteomic changes during MCMV infection revealed by iTRAQ quantitative proteomic analysis in maize

The maize viral pathogen maize chlorotic mottle virus (MCMV) is a devastating disease that causes massive yield losses every year around the world. This work is one of the few papers on the underlying molecular mechanisms of MCMV. The authors used iTRAQ-based comparative proteomics to analyze B73 plants infected with MCMV. The authors identified 972 differentially abundant proteins with the majority of the proteins being involved in photosynthesis and ribosome related pathways. The authors also observed proteins involved in stress responses and redox regulation. In addition, the authors assessed two candidates, ZmPDIL-1 and ZmPrx5, via CMV-induced gene silencing. This is significant because it gives us further insight into the molecular mechanisms of MCMV infection. Brianna Griffin, 2020

Dang, MQ et al. 2020. Int J Mol Sci 21:35
   Proteomic changes during MCMV infection revealed by iTRAQ quantitative proteomic analysis in maize
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Xu, XS, et al. 2021. 56:1-12
   Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery

Single-cell RNA sequencing (scRNA-seq) provides the opportunity to investigate gene expression at a very high resolution. Xu and his colleagues performed scRNA-seq technology and constructed a high-resolution transcriptome atlas of the 5-10 mm developing maize ear inflorescence. They investigated the transcriptional profiles of 12,525 single cells from developing maize ears and predicted 12 meta-clusters that were mostly associated with meristem. This scRNA-seq atlas has been utilized to distinguish redundant from non-redundant paralogs involved in gene networks, build transcriptional regulatory networks, and identify genes associated with maize yield traits. Furthermore, they validated their results by mRNA in situ hybridization and by fluorescence activated cell sorting RNA-seq. Their single-cell gene co-expression networks will facilitate developmental genetics studies by predicting genetic redundancy, integrating transcriptional regulatory networks, and ultimately facilitate maize breeding by identifying candidate genes associated with crop yield traits. This single-cell transcriptome atlas is a valuable resource for the maize community. Meixia Zhao, 2021

Xu et al. map the transcriptional landscape of 12,525 single cells from developing maize ears to create a developmental atlas that shows single-cell RNA-seq map of the inflorescence. This was validated via in situ hybridization and florescence-activated cell sorting (FACS) RNA-seq. The authors also predicted 12 meta-clusters using known markers. With these clusters they found distinct subclusters for meristem, branching, xylem, phloem, determinate lateral organs, and ground tissues. The authors highlight their ability to accurately predict redundancy in a family of maize TPPs that control inflorescence branching. They also show that scRNA-seq marker genes are associated with maize ear traits from GWAS. This study is significant because it is an incredibly useful tool for facilitating genetic studies and breeding strategies. Brianna D. Griffin, 2021

Xu, XS, et al. 2021. 56:1-12
   Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery
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Jing, JL, et al. 2020. Plant Physiol. 0:doi: 10.1104/pp.20.00933
   ZmMTOPVIB enables DNA double-strand break formation and bipolar spindle assembly during maize meiosis

In this article Jing et al. identified ZmTOPVIB (Zm00001d014728) gene in Maize based on homology search from Arabidopsis AtMTOPVIB. Phylogenetic study with other monocot and dicot of the corresponding gene has placed ZmTOPVIB in the monocot clade. This candidate gene is expressed distinctively in the developing tassel, embryo, ear, and endosperm. To functionally characterize its role, they have used two mutant lines, UFMu-07260 (ZmmtopVIB-1) and EMS4-0742ae (ZmmtopVIB-2), of this gene. Interestingly, both mutant lines demonstrate male and female sterility. Subsequently, they have demonstrated that sterility phenotype is happening because of defective meiotic events. From the cell biology context, their experiment suggests the role of ZmTOPVIB in the meiotic bipolar spindle assembly. Taken together, this work highlighted the conserved role of MTOPVIB in bipolar spindle assembly in monocots. Arif Ashraf, 2021

Jing, JL, et al. 2020. Plant Physiol. 0:doi: 10.1104/pp.20.00933
   ZmMTOPVIB enables DNA double-strand break formation and bipolar spindle assembly during maize meiosis
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Luo, HS, et al. 2020. Plant Cell. 0:doi: 10.1105/tpc.20.00043
   Ectopic expression of the transcriptional regulator silky3 causes pleiotropic meristem and sex determination defects in maize inflorescences

Luo et al (2020) identified a maize semi-dominant mutant Silky3 (Si3), which exhibits pleiotropic defects in the inflorescence, including loss of determinacy and identity in meristems and floral organs, as well as the sexual transformation of tassel florets. Positional cloning and functional analysis indicate that si3 encodes a putative transcriptional regulator. Transcriptome analysis and hormone assays reveal that the ectopic expression of si3 disrupts multiple biological processes by modulating gene expression patterns at the floret stage and endogenous homeostasis of JA and GA in the tassel, and exogenous application of JA can restore the sex conversion phenotypes. The research give an example that a mutant with pleiotropic inflorescence phenotypes is attributable to defects in multiple flower-related pathways, and also give the evidence of the hormone crosstalk of JA and GA in maize inflorescence. Yanfang Du, 2021

Luo, HS, et al. 2020. Plant Cell. 0:doi: 10.1105/tpc.20.00043
   Ectopic expression of the transcriptional regulator silky3 causes pleiotropic meristem and sex determination defects in maize inflorescences
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Rogers, AR, et al. 2021. G3. 0:doi: 10.1093/g3journal/jkaa050
   The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment

Rogers et al 2021 used the first three years of trait, environmental, and genetic data from the Genomes to Fields initiative to test the importance of genetic, environmental, and genetic by environmental (GxE) variation in estimating phenotypic variation. By estimating the relative importance of these sources of variation on different traits, breeders can use this information to build better genomic prediction models for their specific programs. Rogers and colleagues estimated additive and dominance genetic variance in both genetic main effects and GxE variances. They found models performed best when including both additive and dominance relationships, even though dominance had smaller estimates. They also used factor analysis to estimate the contributions of environmental variables towards environment main effects and GxE variances, finding weather-based clusters do underlie portions of both. In conclusion, Rogers et al 2021 suggest including these environmental and genomic relationships using this large public dataset and these models may allow breeders to predict performance across untested combinations of genotypes and environments. Samantha Snodgrass, 2021

Rogers, AR, et al. 2021. G3. 0:doi: 10.1093/g3journal/jkaa050
   The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment
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Sun, HY, et al. 2020. New Phytol. 0:doi: 10.1111/nph.16772
   dlf1 promotes floral transition by directly activating ZmMADS4 and ZmMADS67 in the maize shoot apex

During the geographical expansion upon the domestication from teosinte, maize has evolved extraordinary diversity in flowering time to adapt to the environment change from the wide range of latitude. Sun et al deployed the maize-teosinte BC2S3 population to perform a QTL analysis on the phenotype of leaf number and flowering time. They found a previously characterized gene delayed flowering1 (dlf1), encoding a basic leucine zipper transcription factor, was responsible for one of the major QTL loci. The authors have profiled transcriptional changes associated with dlf1-mediated flowering time variation in maize, and identified putative direct targets bound by DLF1 through ChIPseq. Two AP1/FUL subfamily MADS-box genes ZmMADS4 and ZmMADS67, as two intriguing examples of direct targets by DLF1, were further verified by CRISPR knock out for their function as positive regulators of maize flowering. By nucleotide diversity analysis, the authors also found that dlf1 and one of its targets ZmMADS67 were under strong selection, suggesting that they may have played important roles in maize flowering time adaptation. This research provides novel insights into the regulatory hub for the floral transition, and also is an important advance in understanding how maize was able to adapt flowering time to diverse local environments. Zhaobin Dong, 2021

Sun, HY, et al. 2020. New Phytol. 0:doi: 10.1111/nph.16772
   dlf1 promotes floral transition by directly activating ZmMADS4 and ZmMADS67 in the maize shoot apex
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Xu, G, et al. 2020. Nature communications. 11:5539
   Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

DNA methylation is an epigenomic feature that plays an important role in regulating gene expression and phenotypic variation. Xu and his colleagues performed whole-genome sequencing and whole-genome bisulfite sequencing on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to determine the variation and evolution of the methylation landscape during maize domestication. In this research, the authors identified a large number of differentially methylated regions (DMRs) between teosinte and modern maize, between teosinte and landrace, and between landrace and modern maize. They found that although DNA methylation genome-wide is under weak selection, DMRs are enriched in selective sweeps at population levels. In addition, they identified a substantial number of DMRs that are associated with phenotypic variation, and isolated a subset of key domesticated loci, such as vgt1 and tb1, which exhibit the methylation differences under domestication. Finally, this research showed evidence that methylation affects physical interactions between genes and intergenic regulatory elements. These data together advance our understanding of the effects of DNA methylation on maize adaptation and domestication. Meixia Zhao, 2021

Xu, G, et al. 2020. Nature communications. 11:5539
   Evolutionary and functional genomics of DNA methylation in maize domestication and improvement
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Walley, JW; Shen, ZX; McReynolds, MR; Schmelz, EA; Briggs, SP. 2017. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1717519115
   Fungal-induced protein hyperacetylation in maize identified by acetylome profiling

deacetylase inhibitor (HDAC) required for pathogen virulence. In this paper the authors look at hyperacetylation of maize tissue infected with the fungus Cochliobolus carbonum race 1 by acetylome profiling. The authors globally quantified 3,636 proteins and the levels of acetylation at 2,791 sites via mass spectrometry in maize treated with HCT, tox+ and tox-. They found that HCT modulated HDACs to alter acetylation of nonhistone proteins during immune response and that acetylation is a wide-spread post-translational modification. This is significant because it gives us further insight into the molecular mechanisms behind the modulation of histone and nonhistone proteins in response to pathogen infection. Brianna Griffin, 2021

Walley, JW; Shen, ZX; McReynolds, MR; Schmelz, EA; Briggs, SP. 2017. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1717519115
   Fungal-induced protein hyperacetylation in maize identified by acetylome profiling
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Li, Z, et al. 2020. Plant J. 0:doi: 10.1111/tpj.15042
   Single-parent expression drives dynamic gene expression complementation in maize hybrids

Li and colleagues created a population of 80 F1 hybrids from 33 inbred lines representing temperate US breeding pools, sequenced the transcriptomes of these hybrids and inbreds using 5 separate tissues, and investigated a specific pattern of extreme differential expression called Single Parent Expression (SPE). Briefly, SPE is when a gene is expressed in one inbred parent and the hybrid, but not in the other parent. Li and colleagues further delineated SPE caused by underlying presence/absence variation (PAV). They found similar patterns for both PAV SPE and non-PAV SPE: a positive correlation with the genetic distance between inbred parents, highly genotype and tissue specific expression, and depletion for syntenic or experimentally validated functional genes. Using allele specific expression, they demonstrated most non-PAV SPE genes were enriched for cis-regulation. However there were instances of trans-regulation (the silent parental allele being expressed in the hybrid) in all hybrids, though only a few in any one hybrid. Li and colleagues argue that altogether, both types of SPE could contribute to hybrid vigor, but in different ways. Given the importance of hybridization in crop breeding as well as its frequent occurrence in natural populations, applying genomic tools to hybrid populations enables exploration of the genetic consequences and environments this process creates. Samantha Snodgrass, 2021

Li, Z, et al. 2020. Plant J. 0:doi: 10.1111/tpj.15042
   Single-parent expression drives dynamic gene expression complementation in maize hybrids
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Satterlee, JW; Strable, J; Scanlon, MJ. 2020. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.2018788117
   Plant stem-cell organization and differentiation at single-cell resolution

Plants contain stem cells during their life cycle and this feature always provides the advantage of generating new organs. For instance, the visible above ground organs are initiated from the stem cells residing in the shoot apical meristem (SAM) and similar thing is true for hidden half of the plant "root" from root apical meristem (RAM). To understand the developmental process, Scanlon lab isolated cells from SAM and used the protoplasts to do the single cell RNA-seq (scRNA-seq). This unbiased scRNA-seq data is useful for identifying genes for stem cell maintenance, differentiation, and regulation. Additionally, this dataset is helpful to find out the evolutionary conserved or diverged set of genes for SAM. Based on their scRNA-seq data, Satterlee et al. has found that KN1expresses differentially between indeterminate and determinate cell types. Genetic evidence suggests that Kn1-0/+ mutant leaf blade contains misplaced sheath-like identity. Additionally, they have performed scRNA-seq from wild-type and Kn1-0/+; and demonstrated that KN1 and its target gene GA2OX1 are differentially expressed in the indeterminate cells in wild-type. Similar to their demonstrated KN1 example, this dataset will serve as an excellent resource for the maize community to decipher the genetic circuit of shoot morphogenesis. Arif Ashraf, 2021

Satterlee, JW; Strable, J; Scanlon, MJ. 2020. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.2018788117
   Plant stem-cell organization and differentiation at single-cell resolution
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Wang, HH, et al. 2020. Nature communications. 11:5346
   Carotenoids modulate kernel texture in maize by influencing amyloplast envelope integrity

Vitreous endosperm is the highly dense, outer part of the maize endosperm that protects mature kernels from damage. W64A and A619 are two inbred lines which show natural variation in vitreous texture. By crossing W64A and A619, Wang et al. (2020) identified a major QTL, Vitreous endosperm 1 (Ven1), involved in vitreous endosperm formation. Ven1 encodes a B-carotene hydroxylase 3 and is an enzyme specifically localized in the amyloplast envelope in endosperm cells. The authors observed the protein matrix and starch granule formation in NILW64A and NILA619 through SEM and TEM, and found that the organized grid structure of protein bodies and starch granules in NILW64A at late kernel development stage was the key to form vitreous endosperm. Wang et al. continued to screen the suppressor of Ven1A619 to explore the carotenoids biosynthesis correlation with the opaque endosperm phenotype in A619. They also identified several modifiers of Ven1A619 by a genome-wide association study (GWAS) and RNA-seq analysis. The authors' study on the carotenoids biosynthesis correlation with the vitreous phenotype would benefit the corn breeding of high vitamin A content in the future. Fang Bai, 2020

Authors found a major QTL for vitreous endosperm, and they named it Ven1. They cloned ven1 and found it to be represented by gene model Zm00001d026056, previously named hyd3 in maize. Ven1 encodes ��-carotene hydroxylase 3 (HYD3), which hydroxylates the ��-ionone ring of ��-/��-carotene, producing xanthophylls (e.g. lutein and zeaxanthin).

Authors found a major QTL for vitreous endosperm, and they named it Ven1. They cloned ven1 and found it to be represented by gene model Zm00001d026056, previously named hyd3 in maize. Ven1 encodes B-carotene hydroxylase 3 (HYD3), which hydroxylates the B-ionone ring of an alpha/beta carotene, producing xanthophylls (e.g. lutein and zeaxanthin).

Wang, HH, et al. 2020. Nature communications. 11:5346
   Carotenoids modulate kernel texture in maize by influencing amyloplast envelope integrity
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Matschi, S, et al. 2020. 0:doi: 10.1002/pld3.282
   Structure-function analysis of the maize bulliform cell cuticle and its potential role in dehydration and leaf rolling

Dehydration or heat stress induces leaf rolling for maize. In this study, Matschi et al. studied the bulliform cells during the leaf rolling process. Compared to other cells such as pavement cells, bulliform cells have the capacity to shrink more during dehydration or heat stress. These cells have distinct cuticle architecture, structure, composition, and thickness in contrast to other epidermal cells. Although bulliform cells have characteristic cuticles in structure and thickness, they are much more water permeable. Multiple bulliform-enriched mutants (wty2, dek1-D, and Xcl1) have higher cuticular conductance. Mechanistically, higher water permeability of bulliform cells facilitate quick water loss in these cells during dehydration or heat stress and consequent leaf rolling. Arif Ashraf, 2020

Matschi, S, et al. 2020. 0:doi: 10.1002/pld3.282
   Structure-function analysis of the maize bulliform cell cuticle and its potential role in dehydration and leaf rolling
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Le Corre, V et al. 2020. Proc Natl Acad Sci, USA 117:25618-25627
   Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe

Le Corre et al (2020) investigated the population structure and origins of French and Spanish teosinte populations, which are becoming a noxious weed in maize fields. Using FastStructure, PCA, pairwise Fst, and four population tests, French and Spanish teosintes demonstrated closer relatedness to Zea mays spp. mexicana than Zea mays spp. parviglumis with some admixture from domesticated maize. They followed up with TreeMix to reconstruct these phylogenetic relationships while allowing for gene flow between lineages. This detected Dent introgression into both European teosinte populations. Flowering time is a key adaptation for survival and introgression in high latitudes, a trait that has shifted significantly earlier in the European teosintes compared to native tropical parviglumis and mexicana. Le Corre and colleagues found elevated differentiation between the European teosintes and native mexicana on a region of chromosome 8 which overlaps with ZCN8, a major flowering time locus. Additionally, French teosinte populations had introgressed an herbicide resistance allele (ACC1). All together, this suggests adaptive introgression from maize has allowed teosinte populations to expand to Europe with the potential to become a noxious weed. Samantha Snodgrass, 2020

SNP data published here: https://zenodo.org/record/3959138

Le Corre, V et al. 2020. Proc Natl Acad Sci, USA 117:25618-25627
   Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe
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Costa-Neto, G; Fritsche-Neto, R; Crossa, J. 2020. Heredity. 0:Epub
   Nonlinear kernels, dominance, and envirotyping data increase the accuracy of genome-based prediction in multi-environment trials

Costa-Neto et al. explored the integration of genomics and nongenomic sources of variation in genomic prediction models evaluated in two multi-environment maize trials. The authors compared prediction models using different kernels including an implementation of an arc-cosine kernel defined by a covariance matrix that emulates a deep-learning model with one hidden layer and a large number of neurons. Environmental variables were incorporated through a reaction-norm modeling. The Gaussian and Arc-cosine kernels outperformed conventional GBLUP approached in reducing the computational time, and increased the prediction ability for all testing scenarios in tropical maize. The authors further discuss application of the different genomic prediction models to capture non additive affects. Marcio Resende, 2020

Costa-Neto, G; Fritsche-Neto, R; Crossa, J. 2020. Heredity. 0:Epub
   Nonlinear kernels, dominance, and envirotyping data increase the accuracy of genome-based prediction in multi-environment trials
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Tu, XY, et al. 2020. Nature communications. 0:doi: 10.1038/s41467-020-18832-8
   Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors

Tu and colleagues created a high-throughput system of ChIP-seq experiments that allowed them to identify patterns of transcription factor binding sites throughout the maize genome. They investigated 104 transcription factors (TF) using maize leaf protoplasts, resulting in approximately 2 million TF binding peaks and thousands of unique binding site per TF. The authors conducted an exhaustive list of analyses describing the patterns and groupings of these TF binding sites and using them to predict interactions in maize and other species. Notably, Tu et al confirmed that TF binding peaks occur mostly in open chromatin regions (74%) and are densely clustered to cover only about 2% of the genome. Each binding site may bind multiple TFs, indicating coregulation of a gene's transcription by multiple TFs. These regions are under purifying selection in maize and seemingly across species. Previously published GWAS results were also enriched with TF binding sites, indicating the potential importance of non-coding sequence to phenotype. They also performed network analysis, creating a gene regulatory network, verified in part by their ChIP-seq experiments. This network revealed a set of hub genes, some with densely packed TF occupied regions nearby. Further the modules of this network seem to be grouped in biologically meaningful ways, suggesting its utility for future investigations. Finally, Tu and colleagues demonstrated that the TF-to-TF patterns of co-binding were more conserved across rice and sorghum than TF-to-non-TF relationships, suggesting that TF interactions evolve in a hierarchical manner (a few high information relationships under strict purifying selection at the top with more relaxed constraint at lower levels of information). In summary, this method and results open the door for interrogating the non-coding regions of the genome, their evolution and phenotypic impact. Samantha Snodgrass, 2020

Tu, XY, et al. 2020. Nature communications. 0:doi: 10.1038/s41467-020-18832-8
   Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors
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Lu, ZF, et al. 2019. Nature Plants. 12:1250-1259
   The prevalence, evolution and chromatin signatures of plant regulatory elements

The problem with plant genomes is that they are composed primarily of sequences whose primary function appears to be to replicate itself rather than to contribute to the fitness of the plant. That means that coding sequences as well as the sequences important for regulation their expression are embedded in transposable element sequences that may have nothing to do with that regulation. Ricci et al (2019, The prevalence, evolution and chromatin signatures of plant regulatory elements) have used a combination of assays to identify large numbers of regulatory sequences in the maize genome, which will considerably simplify efforts to connect genetically identified cis acting loci with particular sequences. These assays include ATAC, which identifies regions of open chromatin, along with several histone modifications typical for regulatory regions. Not surprisingly, but reassuringly, these regions were enriched for transcription factor binding sites and had reduced nucleotide diversity. Further, Hi-C and HiChIP data supported physical interaction between putative cis regulatory sequences and adjacent genes. The fact that many of the regulatory loci identified here are quite distant from the putative target genes suggests an inflationary model for larger plant genomes, where intervening transposable elements (TEs) expand the distance between these sequences and their targets without necessarily altering the relationships between them. This companion paper (Lu et al. 2019; The prevalence, evolution and chromatin signatures of plant regulatory elements) provides an elegant demonstration of the ways in which these relationships are retained or lost over time. This paper demonstrates that cis-regulatory sequences are wide spread and conserved in plants. Interestingly, the number of these sequences scales with genome size, which is surprising, given that much of the differences in genome size is due to transposon amplification. And, indeed, particularly in larger genomes, species-specific cis regulatory regions are often embedded within transposable elements. This suggests that TEs may contribute new regulatory information that contributes to species diversification, which warms every TE biologist's heart. However, given that TEs can become active and, presumably epigenetically altered, for reasons having nothing to do with gene regulation, the relationship between any given TE and any give gene should be treated as provisional. Together, these two papers provide both specificity and evolutionary context and constitute and important advance in our understanding of the means by which genes are regulated in diverse plant species. Damon Lisch, 2020